tophat gene information

[edeka]

Hi all!
I used tophat2 with the option -G in order to give the gtf file but the output reported the chromosome coordinate. Why? What did I get wrong? How can I obtain the gene information?
Thank you in advance

[dpryan]

tophat2 will always produce alignments in genomic coordinates. If you want alignments in transcriptome coordinates, then use bowtie2 or something similar to align against the transcriptome.

You might also use salmon, sailfish, or Kallisto, which will produce expression metrics directly (I assume that's what you need) and be vastly faster.

[edeka]

tophat2 will always produce alignments in genomic coordinates. If you want alignments in transcriptome coordinates, then use bowtie2 or something similar to align against the transcriptome.

You might also use salmon, sailfish, or Kallisto, which will produce expression metrics directly (I assume that's what you need) and be vastly faster.

Thank you for your answer. So there isn't a tool that allow me to convert the output of TopHat directly in order to have the same SAM file but with informations about the gene?

[dpryan]

You could do that, for example with featureCounts or htseq-count (or bedtools intersect or ...). The question is only what you want to do with the results.

[edeka]

You could do that, for example with featureCounts or htseq-count (or bedtools intersect or ...). The question is only what you want to do with the results.

Thank you (again) for your answer. I am using Ribosome profiling data and I need to have the SAM file with the name gene, position on the gene and the sequence.

[dpryan]

There are already tools for Ribosomal profiling, just use them. Have a look at ribogalaxy (http://ribogalaxy.ucc.ie/) for an example of tools.