Question: Problems With Tophat In Galaxy
0
gravatar for Amit Pande
5.1 years ago by
Amit Pande70
Amit Pande70 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
ADD COMMENTlink modified 5.1 years ago by Jennifer Hillman Jackson25k • written 5.1 years ago by Amit Pande70
0
gravatar for Jennifer Hillman Jackson
5.1 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 5.1 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour