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Old 10-28-2014, 07:57 AM   #5
bbl
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Location: London

Join Date: Jul 2010
Posts: 16
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Thanks very much kmcarr. Indeed what you suspected is what happens!
1st, CEBPA is the gene I'm intereted. From samout by HTSeq-count, reads are mapped to two and three different genes incl. CEBPA. Therefore, they are counted as ambiguous. Actually these reads are also mapped to 1. 'retired' gene, 2. antisense in my .gff ref downloaded from Ensembl.
Since I'm looking at RNAseq samples treated using polyA+tail , I suppose it makes sense to 'manually' modify the .gff ref? For example, remove those pseudogenes, non-coding RNA etc...Would you suggest some way to modify it to be more suitable, if it is a right thing to do?

Many thanks again.
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