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Forum: Bioinformatics 03-13-2017, 01:01 PM
Replies: 8
Views: 1,236
Posted By gringer
Yes, that will probably work. You need to be...

Yes, that will probably work. You need to be careful that you're not excluding reads that hit only partially to the unique regions (i.e. check the HTSeq-count options); any hits to the unique region...
Forum: Bioinformatics 03-13-2017, 11:18 AM
Replies: 8
Views: 1,236
Posted By gringer
This should produce a count table for each...

This should produce a count table for each transcript. It assumes that the most recent version of SAMtools is installed:


cat transcript1.fa transcript2.fa > allTranscripts_myGene.fa # combine...
Forum: Bioinformatics 03-12-2017, 02:24 PM
Replies: 8
Views: 1,236
Posted By gringer
If the gene (or a subsequence of the gene) is not...

If the gene (or a subsequence of the gene) is not genome-unique, then non-specific matches to the gene of interest may happen.

I can't really think of any other cons, except for the whole throwing...
Forum: Bioinformatics 03-12-2017, 03:46 AM
Replies: 8
Views: 1,236
Posted By gringer
If you're looking at a single gene and have the...

If you're looking at a single gene and have the full transcript sequences, why not just map to the transcripts and skip the complicated intron/exon searching?

If you're using Tophat2 for exon...
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