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dzerbino / velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
https://europepmc.org/article/pmc/2336801
GNU General Public License v2.0
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how to extract Unmatched reads paired and Unmatched reads unpaired #41

Closed shrutidabral closed 6 years ago

shrutidabral commented 6 years ago

hello , I am doing a project on metagenomics. I complete the assembly process by using velvet software. Now, i have to find Unmatched reads paired and Unmatched reads unpaired reads in data.

Can you please help me out .

thankyou in advance

dzerbino commented 6 years ago

Hello @shrutidabral ,

What do you mean by unmatched? If you mean reads that did not map into contigs, you can use the '-unused_reads' flag.

HTH,

Daniel

shrutidabral commented 6 years ago

hello Daniel

Thankyou for your reply .

Unmatched reads means unmapped reads .

For that i did this ---

  1. make the indexing file for contigs . [using bowtie command]
  2. Alignment of raw file with index [using bowtie ] command is --- bowtie2 -p 4 --local -x B1 -1 R1.fastq.gz -2 R2.fastq.gz --un unpaired.fq --un-conc paired_unmapped.fq -S R12.sam

after executing this i get unpaired mapped reads and paired mapped reads .

Is this correct way to do this .

dzerbino commented 6 years ago

This is also seems correct.