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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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Extraction of the SSU rRNA sequences that did not assemble into full length sequences #123

Closed aquagenomics closed 3 years ago

aquagenomics commented 4 years ago

Many thanks for this great tool! I was wondering if it would be possible to extract the read sequences corresponding to those that are summarised in the final table (Taxonomic affiliation of unassembled SSU rRNA reads) of the report? I would like to investigate these further, but I couldn't find these sequences (or their fastq IDs) in any of the output files. Thank you!

kbseah commented 4 years ago

Hello @aquagenomics , I'm afraid these reads are not output to a file, only the taxonomy of the hits are counted and summarized in the report. You'll have to re-map the reads onto the assembled/reconstructed sequences and extract the unmapped reads.

kbseah commented 4 years ago

@HRGV i think we can close this issue as there has been no recent activity