Hi Tobias,
In general, you can use *'**NGS: Picard (beta) -> SAM to FASTQ'* to
extract sequences (convert BAM > SAM first), but this tool does not add
in extra sequence based off the reference genome (or pad the associated
quality scores, etc.). I don't know of a Galaxy wrapped tool that does
Hey there,
I am trying to add a custom track of a bed file through Galaxy and i keep
getting this error:
- Error line 325149 of
https://main.g2.bx.psu.edu/root/display_as?id=11632524&display_app=ucsc&authz_method=display_at:
chrM_rCRS not a recognized sequence (note: sequence names are
Please note, this sequence chrM_rCRS does not exist in the human/hg19
genome browser at UCSC. It is not a recognized sequence.
There is a note about this on the gateway page:
http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19
See the paragraph titled: "Note on chrM"
--Hiram
On 9/12/13 1:25 AM
Hi Jen and other galaxy-users,
I was using "Slice BAM" tool on Galaxy to get the alignment overlap with the
targeted intervals. After I got the output BAM file, I used "flagstat" to
get the detailed information of the output BAM file. What I got from
"flagstat" is as following.
"13704486 +
Hi guys,
I am looking for a de novo RNA-seq workflow that uses trinity. Any idea if
there is one available?
Bests,
Carlos
Carlos Canchaya
ccanch...@gmail.com
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