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Question: Problems With Tophat In Galaxy
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gravatar for Amit Pande
5.1 years ago by
Amit Pande • 70
Amit Pande • 70 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.
samtools bam • 752 views
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modified 5.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.1 years ago by Amit Pande • 70
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gravatar for Jennifer Hillman Jackson
5.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.1 years ago by Jennifer Hillman Jackson ♦ 25k
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