Question: Get Reads from a Bin
gravatar for irazoqui.matias
23 months ago by
irazoqui.matias10 wrote:


I've got a series of bins (fasta files) obtained with MetaBAT. Each file has all the contigs that were binned together. My question is if there's any way to extract the reads (from the FastQ file) mapped to each of the contigs in a bin. I have the bam mapping files.

My idea is to reassemble this reads (using something like SPAdes), to see if this results in better contigs (assuming that the reads that were binned together should come from the same genome, the assembly should be better)



metagenomics samtools binning • 545 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by irazoqui.matias10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 463 users visited in the last hour