INTRO

This notebook is part of the ceasmallr (GitHub repo) project, comparing DNA methylation in Crassostrea virginica (Eastern oyster) larvae and zygotes, via whole-genome bisulfite sequencing (WGBS).

Sequences were previously align with Bismark on 20241118.

Next step was to perform deduplication, using Bismark deduplication (Bismark manual).

Note

This notebook was copied from knitted markdown from 02.10-bismark-deduplication.Rmd (commit 1d64c70)/

1 DESCRIPTION

1.1 Inputs

This notebook is a continuation of using Bismark (Krueger and Andrews 2011) to perform methylation analysis. Read alignments were run in 02.00-bismark-bowtie2-alignment.Rmd. This step will perform deduplication (Bismark manual) of the BAM files generated by alignment. Results will be summarized by MultiQC (Ewels et al. 2016).

1.2 Outputs

*_dedup.sorted.bam: Deduplicated, sorted BAMs.
*_dedup.sorted.bam.bai: Deduplicated, sorted BAM index file. Useful for IGV.
*.deduplicated.bam: Deduplicated BAMs. These are not sorted.
*.deduplication_report.txt: Individual summary reports for each deduplication process.
multiqc_report.html: A summary report of the alignment results generated by MultiQC, in HTML format.

Due to the large file sizes of BAMS, these cannot be hosted in the ceasmallr GitHub repo. As such these files are available for download here:

https://gannet.fish.washington.edu/gitrepos/ceasmallr/output/02.10-bismark-deduplication/

2 Create a Bash variables file

This allows usage of Bash variables across R Markdown chunks.

{
echo "#### Assign Variables ####"
echo ""

echo "# Data directories"
echo 'export repo_dir=/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr'
echo 'export output_dir_top=${repo_dir}/output/02.10-bismark-deduplication'
echo 'export alignment_dir="${repo_dir}/output/02.00-bismark-bowtie2-alignment"'
echo ""


echo "# Paths to programs"
echo 'export programs_dir="/home/shared"'
echo 'export bismark_dir="${programs_dir}/Bismark-0.24.0"'
echo 'export bowtie2_dir="${programs_dir}/bowtie2-2.4.4-linux-x86_64"'
echo 'export multiqc="/home/sam/programs/mambaforge/bin/multiqc"'
echo 'export samtools_dir="${programs_dir}/samtools-1.12"'
echo ""

echo "# Set number of CPUs to use"
echo 'export threads=40'


echo "# Print formatting"
echo 'export line="--------------------------------------------------------"'
echo ""
} > .bashvars

cat .bashvars

#### Assign Variables ####

# Data directories
export repo_dir=/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr
export output_dir_top=${repo_dir}/output/02.10-bismark-deduplication
export alignment_dir="${repo_dir}/output/02.00-bismark-bowtie2-alignment"

# Paths to programs
export programs_dir="/home/shared"
export bismark_dir="${programs_dir}/Bismark-0.24.0"
export bowtie2_dir="${programs_dir}/bowtie2-2.4.4-linux-x86_64"
export multiqc="/home/sam/programs/mambaforge/bin/multiqc"
export samtools_dir="${programs_dir}/samtools-1.12"

# Set number of CPUs to use
export threads=40
# Print formatting
export line="--------------------------------------------------------"

3 Deduplication

# Load bash variables into memory
source .bashvars

# Make output directory, if it doesn't exist
mkdir --parents "${output_dir_top}"

cd "${alignment_dir}"

for bam in *_bismark_bt2_pe.bam
do
  # Set stderr filename
  stderr_name=$(echo "${bam}" | awk -F"." '{print $1"."$2"."$3".deduplication.stderr"}')
  
  # Run deduplication
  ${bismark_dir}/deduplicate_bismark \
  --samtools_path ${samtools_dir} \
  --paired \
  --bam \
  --output_dir ${output_dir_top} \
  ${bam} \
  > ${output_dir_top}/${stderr_name} 2>&1
done

4 Sorting

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"


#Sorting for Downstream Applications
find *deduplicated.bam \
| xargs basename -s _R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam \
| xargs -I{} ${samtools_dir}/samtools \
sort {}_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam \
-@ "${threads}" \
-o {}_dedup.sorted.bam

5 Indexing for Downstream Applications

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"
find *dedup.sorted.bam \
| xargs basename -s _dedup.sorted.bam \
| xargs -I{} ${samtools_dir}/samtools \
index {}_dedup.sorted.bam

6 MultiQC

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"

${multiqc} .

7 Checksums

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"

for file in *; do
  if [ "${file}" != "checksums.md5" ]; then
    md5sum "${file}" >> checksums.md5
  fi
done

8 List output files

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"

ls -lh

total 213G
-rw-r--r-- 1 sam sam 455M Nov 14 07:15 CF01-CM01-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 603K Nov 14 08:30 CF01-CM01-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 498M Nov 13 13:56 CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  315 Nov 13 13:56 CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 13:56 CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 4.4G Nov 14 07:19 CF01-CM02-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.4M Nov 14 08:31 CF01-CM02-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 5.9G Nov 13 14:12 CF01-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  319 Nov 13 14:12 CF01-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 14:12 CF01-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 2.1G Nov 14 07:20 CF02-CM02-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 921K Nov 14 08:32 CF02-CM02-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 2.5G Nov 13 14:19 CF02-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  319 Nov 13 14:19 CF02-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 14:19 CF02-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 3.0G Nov 14 07:22 CF03-CM03-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.2M Nov 14 08:33 CF03-CM03-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 3.7G Nov 13 14:29 CF03-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 14:29 CF03-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 14:29 CF03-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 3.4G Nov 14 07:24 CF03-CM04-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.3M Nov 14 08:34 CF03-CM04-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 4.6G Nov 13 14:43 CF03-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  320 Nov 13 14:43 CF03-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 14:43 CF03-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 4.1G Nov 14 07:26 CF03-CM05-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.4M Nov 14 08:35 CF03-CM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 5.4G Nov 13 14:58 CF03-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 14:58 CF03-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 14:58 CF03-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 3.0G Nov 14 07:28 CF04-CM04-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.2M Nov 14 08:36 CF04-CM04-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 3.7G Nov 13 15:08 CF04-CM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  319 Nov 13 15:08 CF04-CM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 15:08 CF04-CM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 5.4G Nov 14 07:33 CF05-CM02-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.6M Nov 14 08:38 CF05-CM02-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 7.5G Nov 13 15:29 CF05-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  320 Nov 13 15:29 CF05-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 15:30 CF05-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 3.5G Nov 14 07:35 CF05-CM05-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.3M Nov 14 08:39 CF05-CM05-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 4.4G Nov 13 15:42 CF05-CM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  319 Nov 13 15:42 CF05-CM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 15:42 CF05-CM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 3.3G Nov 14 07:37 CF06-CM01-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.3M Nov 14 08:40 CF06-CM01-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 4.0G Nov 13 15:52 CF06-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 15:52 CF06-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 15:53 CF06-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 2.6G Nov 14 07:38 CF06-CM02-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.1M Nov 14 08:41 CF06-CM02-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 3.1G Nov 13 16:01 CF06-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 16:01 CF06-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:01 CF06-CM02-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 2.0G Nov 14 07:39 CF07-CM02-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 968K Nov 14 08:41 CF07-CM02-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 2.4G Nov 13 16:08 CF07-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 16:08 CF07-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:08 CF07-CM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 2.2G Nov 14 07:41 CF08-CM03-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 950K Nov 14 08:42 CF08-CM03-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 2.6G Nov 13 16:15 CF08-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  319 Nov 13 16:15 CF08-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:15 CF08-CM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  58M Nov 14 07:41 CF08-CM04-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.1M Nov 14 08:42 CF08-CM04-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  60M Nov 13 16:15 CF08-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  312 Nov 13 16:15 CF08-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:15 CF08-CM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  50M Nov 14 07:41 CF08-CM05-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.1M Nov 14 08:42 CF08-CM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  52M Nov 13 16:15 CF08-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  314 Nov 13 16:15 CF08-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:15 CF08-CM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  16K Nov 14 09:44 checksums.md5
-rw-r--r-- 1 sam sam 2.8G Nov 14 07:42 EF01-EM01-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.2M Nov 14 08:43 EF01-EM01-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 3.5G Nov 13 16:25 EF01-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 16:25 EF01-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:25 EF01-EM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 3.0G Nov 14 07:44 EF02-EM02-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.2M Nov 14 08:44 EF02-EM02-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 3.7G Nov 13 16:35 EF02-EM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 16:35 EF02-EM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:35 EF02-EM02-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 2.0G Nov 14 07:45 EF03-EM03-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 897K Nov 14 08:45 EF03-EM03-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 2.3G Nov 13 16:41 EF03-EM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 16:41 EF03-EM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:41 EF03-EM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 4.1G Nov 14 07:47 EF03-EM04-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.4M Nov 14 08:46 EF03-EM04-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 5.1G Nov 13 16:55 EF03-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  319 Nov 13 16:55 EF03-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 16:56 EF03-EM04-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 4.1G Nov 14 07:50 EF03-EM05-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.5M Nov 14 08:47 EF03-EM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 5.4G Nov 13 17:10 EF03-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 17:10 EF03-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 17:11 EF03-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 1.1G Nov 14 07:50 EF04-EM04-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 600K Nov 14 08:47 EF04-EM04-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 1.2G Nov 13 17:14 EF04-EM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  317 Nov 13 17:14 EF04-EM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 17:14 EF04-EM04-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 4.9G Nov 14 07:55 EF04-EM05-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.5M Nov 14 08:49 EF04-EM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 6.8G Nov 13 17:33 EF04-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  320 Nov 13 17:33 EF04-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 17:33 EF04-EM05-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 3.1G Nov 14 07:57 EF05-EM01-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.2M Nov 14 08:50 EF05-EM01-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 4.1G Nov 13 17:45 EF05-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  318 Nov 13 17:45 EF05-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 17:45 EF05-EM01-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 702M Nov 14 07:57 EF05-EM05-Zygote_dedup.sorted.bam
-rw-r--r-- 1 sam sam 567K Nov 14 08:50 EF05-EM05-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 756M Nov 13 17:47 EF05-EM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  316 Nov 13 17:47 EF05-EM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 17:47 EF05-EM05-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 5.0G Nov 14 08:02 EF05-EM06-Larvae_dedup.sorted.bam
-rw-r--r-- 1 sam sam 1.6M Nov 14 08:52 EF05-EM06-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam 7.0G Nov 13 18:07 EF05-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam
-rw-r--r-- 1 sam sam  320 Nov 13 18:07 EF05-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam 3.4K Nov 13 18:07 EF05-EM06-Larvae_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam 4.9G Nov 14 08:06 EF06-EM01-Larvae_dedup.sorted.bam
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drwxr-xr-x 2 sam sam 4.0K Nov 14 09:30 multiqc_data
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Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics 32 (19): 3047–48. https://doi.org/10.1093/bioinformatics/btw354.

Krueger, Felix, and Simon R. Andrews. 2011. “Bismark: A Flexible Aligner and Methylation Caller for Bisulfite-Seq Applications.” Bioinformatics 27 (11): 1571–72. https://doi.org/10.1093/bioinformatics/btr167.