Output RNA-seq reads that don't map to the transcriptome
Hi everyone. I am trying to identify reads from human RNA-seq data the are NOT mapped to the transcriptome. Is there a way to get a software like SoapSplice to output this kind of reads?
Thanks in advance.
Arturo
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arturo.didonna •
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Why not just use STAR/tophat/whatever to map as normal and then use htseq-count and parse the output of the -o option? You'll then have all alignments annotated with whether they align to a feature (just grepping for something like "no_feature" should then find all of the alignments you're after).
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Devon Ryan
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Once you have transcriptome ref-seq and its bowtie index, run tophat2, and then from output unmapped.bam is consisting the reads you are interested in , isn't it?