How I Remove Ncrna From Raw Reads?
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8.6 years ago
chimerajit • 0

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.

bioinformatics • 1.3k views
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8.6 years ago
Ido Tamir 5.2k

The ouptut 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

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Oh! automatic link creation for SAM very nice

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thanks a lot hope this will work for me

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