Hi All,
After aligning to the genome, we figured out that there are lot of globin transcripts in our data due to the experimental error while isolating RNA. I am aware that we can mask specific transcripts during the alignment step so that they won't show up in the final count files. Can one suggest me which aligner can be used for such making procedure. I generally use STAR aligner for RNA-Seq.
Thanks a lot.
cheers,
Aravind
There might be countless solutions for that, let me just tell you the first that came to my mind, and I would use that.
You want to extract the globin sequences and use the rest, so in other word you want to separate your reads to two sets, one with hits on globin genes and the rest, if I am right.
There is a program suite called MIRA ( MIRA4 is the current version ). Along with the main program that you will not want to use (that is for whole genome assembly) there are very handy utility tools there. One of these is mirabait, which is exactly for your your purpose, that is, fishing out sequences from a big bunch, according to similarity to a query set. Check it out and see how it fits.
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_mutils_bait
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