Hello Amit,

The output files created by Tophat are listed on the tool form: accepted_hits.bam, junctions.bed, insertions.bed and deletions.bed

This is NGS data input? Do you mean that no data in the results (accepted_hits.bam - could convert to SAM to check) include the "XS" tag?

If no result/tags, then spliced data is not mapping. Reviewing the advanced parameters would be helpful, but I would start with the quality of the input data (run FastQC). It may be that some trimming is needed (run Trim).

Thanks,

Jen
Galaxy team

On 11/7/13 1:53 AM, Amit Pande wrote:

Hi,

I am trying to align long RNA fatsq formatted files from ENCODE project generated by CSHL.

The problem I am encountering is that there is no XS file being generated which can be taken for further processing with samtools.

Kindly help.

warm regards,

Amit.
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