Question: Masking reads that map to two genomes in galaxy
gravatar for k.rattigan.1
2.5 years ago by
k.rattigan.10 wrote:

I've gotten RNAseq data (paired end Illumina) that is from two different species. I've used Tophat on the two genomes seperately and I get 42 and 5 million reads respectively that are concordantly aligned. I was wondering if there was a way of masking reads that map to both species

Thanks for any help or advice you can give.

rna-seq tophat • 595 views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.5 years ago by k.rattigan.10
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You could compare the mapped sequence identifiers and filter out sequences that way. Tools in the groups Text Manipulation, Filter and Sort, plus Join, Subtract and Group contain many basic operations that can be run together, much like line-command bioinformatics.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour