Question: Re: Trouble Getting Tophat To Run On Built-In Index Genome
0
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Noa,
There are two issues: Using the correct genome and setting up paired
data properly.
1 - Custom genomes
Perhaps you have discovered this already, but to set the TopHat tool
form to use a custom reference genome from the history, this option:
"Will you select a reference genome from your history or use a built-
in
index?:"
Should be set to:
"Use one from the history"
The form will then refresh, offering a new pull-down menu under the
option:
"Select the reference genome:"
that now includes datasets from the right history panel (instead of
genome names, native to Galaxy). Select the fasta formatted custom
reference genome and initiate the job.
I am not sure how you were able to get 100% mapped if the wrong genome
was used ..., perhaps the genome you ended up mapping to was similar
to
the one you wanted to map to (different releases of the same species)?
Or maybe you did use the genome from the history after all? Moving on
to
Cufflinks might give you some more information about the map quality
(especially if used with a reference gene GTF file).
2 - Mated pairs
Flagstat is not the best tool for the latest RNA-seq data. Instead,
try
"NGS: Picard (beta) -> SAM/BAM Alignment Summary Metrics or BAM Index
Statistics".
Hopefully this has been worked out or this is helpful! Apologies for
the
delay in reply, this question was overlooked during the holiday
shuffle,
Best,
Jen
Galaxy team
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support