Looking for no-hits within Sample & Reference Genome

[amarth]

Hi pals,

This is amarth, and my question is:

How can I extract no-hits data from the alignment of the sample, with the reference genome?


My main goal is not to visualize differential expression of genes (maybe it is, as a partial goal), but the main one, is to identify genes (maybe from a virus) expressed in all the transcript RNA of a sample with symptoms of the disease, but not in a healthy sample.

[sisch]

How can I extract no-hits data from the alignment of the sample, with the reference genome?

Can you give additional information on the setup.
What kind of alignment do you have, SAM/BAM, BLAST, BLAT, etc.?

In general, if you have a set of mappable transcripts M and a set of all transcripts from the healthy reference T you could just subtract the set T from M to get all those transcripts that are in your sequencing but not in the healthy reference.

Set operations can be done in R or even in bash. There is an extensive explanation here: http://www.catonmat.net/blog/set-ope...in-unix-shell/

Best,
Simon