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