Genome Browser to visualize RNA-Seq Data

[Dolphin22]

Hey there,

I am looking for a Genome Browser that is able to visualize my Helicos sequencing data (BAM-files) on the Arabidopsis transcriptome (TAIR10) and additionally having the possibility to export the number of reads aligned to each gene into a text or excel file.

Up till now I tried Integrated genome browser and Integrative genomics viewer. But they do not seem to have this feature.

If somebody knows a good one pls tell me

[Peter Bjarke Olsen]

Artemis is able visualize. Not sure about the exports. See http://www.sanger.ac.uk/resources/software/artemis/

Best regards,

Peter

[chadn737]

Hey there,

I am looking for a Genome Browser that is able to visualize my Helicos sequencing data (BAM-files) on the Arabidopsis transcriptome (TAIR10) and additionally having the possibility to export the number of reads aligned to each gene into a text or excel file.

Up till now I tried Integrated genome browser and Integrative genomics viewer. But they do not seem to have this feature.

If somebody knows a good one pls tell me

I would recommend skipping a browser for this step and use HTSeq-count or BEDTools. I generally consider HTSeq-count the easier of the two as you don't have to bother with everything being in BED format and can work with a SAM and GTF/GFF file.

[Dolphin22]

@chadn737 Sounds good thanks for the advice!!

Do you a source where I can download a binary fo HTSeq for Windows? I was looking at http://pypi.python.org/pypi/HTSeq but I could not find a binary.

Googeling also did not retrieve anaything

[chadn737]

There isn't a binary. It is part of a package of python scripts. You will need to have python and the necessary prerequisites.