How I Remove Ncrna From Raw Reads?

Question

[chimerajit]

to remove ncRNA from raw reads I use Bowtie2 by making a ncRNA index. But after aligning with this index I want to save the reads those are showing no match with this index. how do I do that. I am using fedora 16. Please help me to solve the problem.

Answer 1

[Ido Tamir]

The output option section shows:

• --un which outputs unpaired unaligned reads to a file
• --un-conc which outputs paired-end reads that fail to align concordantly into a file

or you take the SAM/BAM output and filter it yourself by the flags

[Ido Tamir]

Oh! automatic link creation for SAM very nice

[Ram]

I've removed such auto-created links as most of the time, they look like spam by linking every mention of SAM or BAM to the SAM spec.

[chimerajit]

thanks a lot hope this will work for me