I am trying to align long RNA fatsq formatted files from ENCODE
generated by CSHL.
The problem I am encountering is that there is no XS file being
which can be taken for further processing with samtools.
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"
If no result/tags, then spliced data is not mapping. Reviewing the
advanced parameters would be helpful, but I would start with the
of the input data (run FastQC). It may be that some trimming is needed