I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's
output files, such as percentage of reads mapped to the genome...but I
not sure how to do that.
I am also trying to visualize the BAM file by IGB but the following
message appears : " Failed to authenticate to the server".
Anyone can help with these issues?
Thank so much
The tool " NGS: Picard (beta) -> SAM/BAM Alignment Summary Metrics"
be the tool you are looking for. There are others in this tool group
that added up numbers in BAM or SAM files, and SAMTools has
so you could create you own calculation with one of those, plus a
on the fastq inputs, and the "Compute" tool, if it is not exactly
Are you using the public Main Galaxy instance at
https://main.g2.bx.psu.edu/ usegalaxy.org) clicking over to connect
the Genomic HyperBrowser, via web? Or are you doing something else?
you give this another try this morning and see if it is working?
Hopefully the first part helped, let us know about the second,
Galaxy Support and Training