sRNA-seq Alignments - E5 Coral A.pulchra P.meandrina Using ShortStack on Mox

2023
E5
Author

Sam White

Published

June 28, 2023

Steven had asked that I align the coral E5 sRNA-seq reads using ShortStack (GitHub Issue). I previously trimmed the sRNA-seq reads to 35bp in length (notebook). Next up was to actually perform the alignments using ShortStack4. A.pulchra was aligned to the P.millepora genome, per this GitHub Issue. This was run on Mox.

NOTE: Up to this point, I’ve processed all three species simultaneously for which we currently have sRNA-seq data: A.pulchra, P.evermanni, and P.meandrina. However, we currently haven’t decided on the canonical genome to use for P.evermanni (GitHub Issue), so P.evermanni is not included in this analysis.

Skip to RESULTS.

SLURM script (GitHub):

#!/bin/bash
## Job Name
#SBATCH --job-name=20230628-E5_coral-ShortStack-sRNAseq
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-00:00:00
## Memory per node
#SBATCH --mem=500G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq

### E5 sRNA-seq alignments using trimmed reads from 20230620 with ShortStack.

### Expects FastQ read directory paths to be formatted like:

# /gscratch/srlab/sam/data/P_meandrina/sRNAseq/trimmed

### Uses trimmed reads from 20230620. Expect FastQ filename format like:

# *flexbar_trim.20230621_[12]*.fastq.gz


###################################################################################
# These variables need to be set by user

## Assign Variables

# Set FastQ filename patterns
fastq_pattern='**flexbar_trim.20230621*.fastq.gz'

# Set number of CPUs to use
threads=40


# Input/output files
fastq_checksums=input_fastq_checksums.md5
sRNA_FastA="/gscratch/srlab/sam/data/miRBase/20230628-miRBase-mature.fa"

# Data directories
reads_dir=/gscratch/srlab/sam/data

## Inititalize arrays
trimmed_fastq_array=()



# Species array (must match directory name usage)
species_array=("A_pulchra" "P_meandrina")

# Programs associative array
declare -A programs_array
programs_array=(
    [ShortStack]="ShortStack"
    )

# Genomes associative array
declare -A genomes_array
genomes_array=(
    [A_pulchra]="/gscratch/srlab/sam/data/A_millepora/genomes/GCF_013753865.1_Amil_v2.1_genomic.fasta" \
    [P_meandrina]="/gscratch/srlab/sam/data/P_meandrina/genomes/Pocillopora_meandrina_HIv1.assembly.fasta"
    )


###################################################################################

# Exit script if any command fails
set -e

# Load Anaconda
# Uknown why this is needed, but Anaconda will not run if this line is not included.
. "/gscratch/srlab/programs/anaconda3/etc/profile.d/conda.sh"

# Activate flexbar environment
conda activate ShortStack4_env


# Set working directory
working_dir=$(pwd)

for species in "${species_array[@]}"
do
    ## Inititalize arrays
    trimmed_fastq_array=()


    echo "Creating ${species} directory ..." 

    mkdir --parents "${species}"

    # Change to species directory
    cd "${species}"


    # ShortStack output directory
    output_dir=$(pwd)

    echo "Now in ${PWD}."

    # Sync raw FastQ files to working directory
    echo ""
    echo "Transferring files via rsync..."

    rsync --archive --verbose \
    ${reads_dir}/${species}/sRNAseq/trimmed/${fastq_pattern} .

    echo ""
    echo "File transfer complete."
    echo ""

    ### Run ShortStack ###

    ### NOTE: Do NOT quote trimmed_fastq_list
    # Create array of trimmed FastQs
    trimmed_fastq_array=(${fastq_pattern})

    # Pass array contents to new variable as space-delimited list
    trimmed_fastq_list=$(echo "${trimmed_fastq_array[*]}")

    echo "Beginning ShortStack on ${species} sRNAseq using genome FastA:"
    echo "${genomes_array[${species}]}"
    echo ""

    ## Run ShortStack ##
    ${programs_array[ShortStack]} \
    --genomefile "${genomes_array[${species}]}" \
    --readfile ${trimmed_fastq_list} \
    --known_miRNAs ${sRNA_FastA} \
    --dn_mirna \
    --threads ${threads} \
    --outdir ${output_dir}/ShortStack_out

    echo "ShortStack on ${species} complete!"
    echo ""


    ######## Create MD5 checksums for raw FastQs ########

    for fastq in ${fastq_pattern}
    do
        echo "Generating checksum for ${fastq}"
        md5sum "${fastq}" | tee --append ${fastq_checksums}
        echo ""
    done

    ######## END MD5 CHECKSUMS ########

    ######## REMOVE INPUT FASTQS ########
    echo "Removing input FastQs."
    echo ""
    rm ${fastq_pattern}
    echo "Input FastQs removed."
    echo""

    echo "Now moving back to ${working_dir}."
    cd "${working_dir}"
    echo ""

done

####################################################################

# Capture program options
if [[ "${#programs_array[@]}" -gt 0 ]]; then
  echo "Logging program options..."
  for program in "${!programs_array[@]}"
  do
    {
    echo "Program options for ${program}: "
    echo ""
    # Handle samtools help menus
    if [[ "${program}" == "samtools_index" ]] \
    || [[ "${program}" == "samtools_sort" ]] \
    || [[ "${program}" == "samtools_view" ]]
    then
      ${programs_array[$program]}

    # Handle DIAMOND BLAST menu
    elif [[ "${program}" == "diamond" ]]; then
      ${programs_array[$program]} help

    # Handle NCBI BLASTx menu
    elif [[ "${program}" == "blastx" ]]; then
      ${programs_array[$program]} -help

    # Handle fastp menu
    elif [[ "${program}" == "fastp" ]]; then
      ${programs_array[$program]} --help
    else
    ${programs_array[$program]} -h
    fi
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
  } &>> program_options.log || true

    # If MultiQC is in programs_array, copy the config file to this directory.
    if [[ "${program}" == "multiqc" ]]; then
      cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml
    fi
  done
fi


# Document programs in PATH (primarily for program version ID)
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log

RESULTS

Run time seemed relatively fast; just a bit over 4hrs:

Screencap showing ShortStack runtime on Mox of 4hrs 11mins 59secs

The results and links to various files are below. At this time, I have not done any evaluation of the results, nor have I looked into the ShortStack documentation to read how the results are formatted; will leave this for a future date and/or somebody else.

Output folder:

A.pulchra

  • Results files:

    readfile mapping_type read_length count
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam U <21 120030
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam U 21 43333
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam U 22 105592
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam U 23 65039
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam U 24 84409
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam U >24 3636233
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam P <21 196501
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam P 21 61672
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam P 22 73193
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam P 23 69147
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam P 24 73631
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam P >24 5674586
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam R <21 25655
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam R 21 11222
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam R 22 12916
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam R 23 14482
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam R 24 19433
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam R >24 1400108
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam H <21 7685
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam H 21 2697
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam H 22 3260
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam H 23 3166
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam H 24 4394
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam H >24 238409
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam N <21 104184
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam N 21 60191
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam N 22 52988
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam N 23 59083
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam N 24 76366
    /gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam N >24 5252357

    • Counts.txt (1.3M)

      • MD5: 593069a45787e4176c5e17efe3b87d49
    Coords Name MIRNA sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1 sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2 sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1 sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2 sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1 sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_2 sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_1 sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_2 sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_1 sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_2
    NC_058066.1:152483-152906 Cluster_1 N 1 3 126 137 1 2 2 2 2 3
    NC_058066.1:161082-161790 Cluster_2 N 46 57 48 54 210 319 33 25 190 270
    NC_058066.1:203244-203650 Cluster_3 N 17 15 37 30 11 15 15 10 41 33
    NC_058066.1:204535-205150 Cluster_4 N 6 6 270 254 18 16 12 6 56 59
    NC_058066.1:205746-206966 Cluster_5 N 82 93 450 453 66 71 253 239 239 127
    NC_058066.1:210855-211344 Cluster_6 N 340 351 213 210 83 81 0 1 656 647
    NC_058066.1:349656-351297 Cluster_7 N 497 510 1246 1247 841 772 768 762 19 21
    NC_058066.1:351491-353439 Cluster_8 N 3253 3186 2069 2014 2158 2159 2113 2084 169 174
    NC_058066.1:776275-776779 Cluster_9 N 0 0 318 280 10 11 58 61 180 175

    • Results.txt (2.8M)

      • MD5: 0ae9d3267579e8614e57a73a3490430d
    Locus Name Chrom Start End Length Reads UniqueReads FracTop Strand MajorRNA MajorRNAReads Short Long 21 22 23 24 DicerCall MIRNA known_miRNAs
    NC_058066.1:152483-152906 Cluster_1 NC_058066.1 152483 152906 424 279 77 0.512544802867383 . UAAGUACUUUAUCAACUAACUCUAGGCA 77 3 260 0 3 0 13 N N NA
    NC_058066.1:161082-161790 Cluster_2 NC_058066.1 161082 161790 709 1252 475 0.623801916932907 . AGUCGACGAAUUUGCCAUGAAGCUAGUA 71 39 1129 26 10 5 43 N N NA
    NC_058066.1:203244-203650 Cluster_3 NC_058066.1 203244 203650 407 224 112 0.535714285714286 . UUCUGACUCUAUUAGCAACGAAGACUUU 38 2 217 2 1 0 2 N N NA
    NC_058066.1:204535-205150 Cluster_4 NC_058066.1 204535 205150 616 703 343 0.500711237553343 . UCCCAACACGUCUAGACUGUACAAUUUCU 33 4 682 2 0 7 8 N N NA
    NC_058066.1:205746-206966 Cluster_5 NC_058066.1 205746 206966 1221 2073 732 0.535455861070912 . CAAAAGAGCGGACAAAAUAGUCGACAGAUU 152 15 1999 8 6 13 32 N N NA
    NC_058066.1:210855-211344 Cluster_6 NC_058066.1 210855 211344 490 2582 667 0.497676219984508 . UAAUACUUGUAGUGAAGGUUCAAUCUCGA 97 17 2355 13 18 39 140 N N NA
    NC_058066.1:349656-351297 Cluster_7 NC_058066.1 349656 351297 1642 6683 2375 0.501571150680832 . UCAGCUUGGAAAUGACAGCUUUUGACGU 294 53 6417 22 45 44 102 N N NA
    NC_058066.1:351491-353439 Cluster_8 NC_058066.1 351491 353439 1949 19379 3490 0.498632540378761 . UUUCAAAUCAAAGAUCUUCGCAACGAUGA 1115 135 18526 59 101 247 311 N N NA
    NC_058066.1:776275-776779 Cluster_9 NC_058066.1 776275 776779 505 1093 284 0.517840805123513 . UGUUAUUGUCUUUGAGUGCCCAAAUGUGU 64 3 1080 2 3 2 3 N N NA

  • GFFs:

  • BAMs:

P.meandrina

  • Results files:

    • Counts.txt (684K)

      • MD5: 45c7fa265a74c685ce60848447fa4566
      Coords Name MIRNA sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1 sRNA-POC-47-S1-TP2.flexbar_trim.20230621_2 sRNA-POC-48-S1-TP2.flexbar_trim.20230621_1 sRNA-POC-48-S1-TP2.flexbar_trim.20230621_2 sRNA-POC-50-S1-TP2.flexbar_trim.20230621_1 sRNA-POC-50-S1-TP2.flexbar_trim.20230621_2 sRNA-POC-53-S1-TP2.flexbar_trim.20230621_1 sRNA-POC-53-S1-TP2.flexbar_trim.20230621_2 sRNA-POC-57-S1-TP2.flexbar_trim.20230621_1 sRNA-POC-57-S1-TP2.flexbar_trim.20230621_2
      Pocillopora_meandrina_HIv1___Sc0000000:9091-9526 Cluster_1 N 1828 1784 1393 1412 1842 1812 3219 3286 3565 3477
      Pocillopora_meandrina_HIv1___Sc0000000:53578-53997 Cluster_2 N 24 24 52 53 67 67 53 55 95 91
      Pocillopora_meandrina_HIv1___Sc0000000:146768-147202 Cluster_3 N 3 248 2 73 0 116 0 107 5 226
      Pocillopora_meandrina_HIv1___Sc0000000:150243-150718 Cluster_4 N 437 422 691 676 813 804 692 700 1021 1007
      Pocillopora_meandrina_HIv1___Sc0000000:173728-174150 Cluster_5 N 171 167 169 167 269 271 317 318 336 334
      Pocillopora_meandrina_HIv1___Sc0000000:187648-188072 Cluster_6 N 8 7 16 13 28 27 59 72 76 76
      Pocillopora_meandrina_HIv1___Sc0000000:485727-486254 Cluster_7 N 114 112 98 96 49 50 165 168 270 259
      Pocillopora_meandrina_HIv1___Sc0000000:525310-527341 Cluster_8 N 3753 3707 1260 1254 4711 4627 2811 2878 2607 2572
      Pocillopora_meandrina_HIv1___Sc0000000:541262-541723 Cluster_9 N 127 130 86 91 85 96 331 317 85 87

    • Results.txt (1.4M)

      • MD5: 7b96db202d049a53f154ee3fc1fcda08
      Locus   Name    Chrom   Start   End Length  Reads   UniqueReads FracTop Strand  MajorRNA    MajorRNAReads   Short   Long    21  22  23  24  DicerCall   MIRNA   known_miRNAs
Pocillopora_meandrina_HIv1___Sc0000000:9091-9526    Cluster_1   Pocillopora_meandrina_HIv1___Sc0000000  9091    9526    436 23618   903 0.501566601744432   .   UCUACCACUGAGCUAUACCCCC  3810    2853    9677    1223    8614    359 892 N   N   NA
Pocillopora_meandrina_HIv1___Sc0000000:53578-53997  Cluster_2   Pocillopora_meandrina_HIv1___Sc0000000  53578   53997   420 581 27  0.500860585197935   .   GCCUAAGUUGCUUGGAACA 142 577 4   0   0   0   0   N   N   NA
Pocillopora_meandrina_HIv1___Sc0000000:146768-147202    Cluster_3   Pocillopora_meandrina_HIv1___Sc0000000  146768  147202  435 780 108 0.971794871794872   +   AGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 267 2   773 4   0   1   0   N   N   NA
Pocillopora_meandrina_HIv1___Sc0000000:150243-150718    Cluster_4   Pocillopora_meandrina_HIv1___Sc0000000  150243  150718  476 7263    645 0.496902106567534   .   UUAUGUGAUGAGUAUGUUAAUGUACUCUCUGAGC  566 1692    2932    1272    749 280 338 N   N   NA
Pocillopora_meandrina_HIv1___Sc0000000:173728-174150    Cluster_5   Pocillopora_meandrina_HIv1___Sc0000000  173728  174150  423 2519    134 0.500992457324335   .   CAACCAGAUCACAGCAAUCAAA  438 212 8   83  1269    887 60  22  N   NA
Pocillopora_meandrina_HIv1___Sc0000000:187648-188072    Cluster_6   Pocillopora_meandrina_HIv1___Sc0000000  187648  188072  425 382 74  0.523560209424084   .   AUAAAUGUCACUACAAGAAACCUGAAAUCGU 25  1   366 2   2   4   7   N   N   NA
Pocillopora_meandrina_HIv1___Sc0000000:485727-486254    Cluster_7   Pocillopora_meandrina_HIv1___Sc0000000  485727  486254  528 1381    391 0.503982621288921   .   UUGCACUAGAACAGACUGUGCUUCCAUAUCAGCUG 152 132 1174    14  22  6   33  N   N   NA
Pocillopora_meandrina_HIv1___Sc0000000:525310-527341    Cluster_8   Pocillopora_meandrina_HIv1___Sc0000000  525310  527341  2032    30180   6208    0.498939695162359   .   UUUUCGUCACUUUCUUCAGCCUCAGAGU    973 277 27960   102 211 625 1005    N   N   NA
Pocillopora_meandrina_HIv1___Sc0000000:541262-541723    Cluster_9   Pocillopora_meandrina_HIv1___Sc0000000  541262  541723  462 1435    283 0.500348432055749   .   UUGGACGAAAUUUCGAGGUUCACACUCGUU  86  0   1425    0   7   2   1   N   N   NA

    • alignment_details.tsv (48K)

      • MD5: b89a4d5f7d1c49fcc8b3c31fdb316837
      readfile    mapping_type    read_length count
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  U   <21 277334
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  U   21  114752
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  U   22  331234
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  U   23  133358
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  U   24  46856
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  U   >24 1441069
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  P   <21 472110
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  P   21  109577
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  P   22  119506
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  P   23  96527
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  P   24  73770
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  P   >24 3922569
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  R   <21 270975
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  R   21  95814
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  R   22  130073
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  R   23  82638
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  R   24  190938
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  R   >24 1254706
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  H   <21 20811
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  H   21  5811
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  H   22  5117
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  H   23  5552
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  H   24  5909
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  H   >24 47393
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  N   <21 122944
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  N   21  59503
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  N   22  101407
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  N   23  92953
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  N   24  117111
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam  N   >24 5315658

  • GFFs:

  • BAMs: