After completing the taxonomic comparisons of 201002558-2729-Q7 and 6129-403-26-Q7 on 20201002, I decided to extract reads assigned to the following taxa for further exploration (primarily to identify contigs/scaffolds in our cbai_genome_v1.0.fasta (19MB).
Used MEGAN6 to extract reads from the MEGAN6 RMA6 files from 201002558-2729-Q7 taxonomic assignments on 20200928.
RESULTS
Output folders:
20201007_cbai_megan-read-extractions_6129-403-26-Q7/
20201007_cbai_megan-read-extractions_6129-403-26-Q7/6129-403-26-Q7_summarized-reads-Arthropoda.fasta
20201007_cbai_megan-read-extractions_6129-403-26-Q7/6129-403-26-Q7_summarized-reads-Alveolata.fasta
Here are stats on the extracted FastAs, generated with the BBTools
stats.shscript, using theformat=5output format.NOTE: The L50 and N50 values are swapped in the original output! I have manually changed the column labels to redue confusion. This seems to be a long-standing “bug” in this program, and exists in all output format options.
file n_contigs contig_bp gap_pct ctg_L50 ctg_N50 ctg_L90 ctg_N90 ctg_max gc_avg gc_std 201002558-2729-Q7_summarized-reads-Aquifex_sp..fasta 280 444988 0 70 2050 196 846 8255 0.40435 0.03572 201002558-2729-Q7_summarized-reads-Arthropoda.fasta 1850 3398935 0 432 2495 1294 957 19092 0.42579 0.06937 201002558-2729-Q7_summarized-reads-Enterospora_canceri.fasta 1554 2409480 0 349 2216 1074 771 8849 0.40246 0.04166 201002558-2729-Q7_summarized-reads-Sar.fasta 6 14692 0 3 2729 5 1559 3969 0.49442 0.04577 6129-403-26-Q7_summarized-reads-Alveolata.fasta 461 1753568 0 95 5681 293 1997 19921 0.45848 0.06894 6129-403-26-Q7_summarized-reads-Aquifex_sp..fasta 4187 20911232 0 877 7839 2615 2662 32879 0.41532 0.03779 6129-403-26-Q7_summarized-reads-Arthropoda.fasta 29649 160465929 0 6130 8336 18669 2802 51326 0.43271 0.05866 6129-403-26-Q7_summarized-reads-Enterospora_canceri.fasta 18111 83280155 0 3589 7369 11022 2357 49825 0.41499 0.04149
Now, I’ll try aligning these reads to the cbai_genome_v1.0 using BLAST to see if I can identify which contigs/scaffolds belong to each of these taxa.