Transcriptome alignments to genome alignments

[epicardi]

Hi All,
I'm mapping RNA-Seq reads onto the human transcriptome (gencode set) and I would to translate transcript coordinates in genomic coordinates.
I tried RSEM and, in particular, the tool rsem-tbam2gbam but I got the following error:
rsem-tbam2gbam: BamConverter.h:154: void BamConverter:rocess(): Assertion `cqname != ((char*)((b)->data))' failed.

and I don't know how to fix it.
Is there an alternative way?

Many Thanks,

Ernesto

[dpryan]

Why not just use tophat2 or STAR?

[epicardi]

I would to avoid mapping errors near exon-exon junctions. Both tools you propose are quite efficient. tophat2 should use transcriptome information but not sure if is alone.

[dpryan]

Well you can have tophat2 map only to the transcriptome, if that's what you mean by "not sure if is alone".

[epicardi]

Thanks, I could try even though I prefer GSNAP. In this case I have to translate transcriptome coordinates to genome coordinates. I would to save time if a tool is already available, otherwise a custom script could be the solution.

[super0925]

Well you can have tophat2 map only to the transcriptome, if that's what you mean by "not sure if is alone".

What is different between mapping to genome and mapping to transcriptome?
when to genome and when to transcriptome?
Is Tophat could do both?
Thank you

[yueluo]

What is different between mapping to genome and mapping to transcriptome?
when to genome and when to transcriptome?
Is Tophat could do both?
Thank you

A similar question has been asked recently.

http://seqanswers.com/forums/showthread.php?t=41169