Hello Matt,
I am not sure what you mean by an annotated genome, would you be able to
send more details?
Meanwhile, I can let you know that the tools that use a reference genome
(custom or native) all expect a fasta formatted input and use the data
directly or create indexes from the data. An
I don't know anything about the tool or parameters in question , but it looks
like the expected output filename is well formatted enough that you can derive
it from the input filename and parameters.
You could write a small python wrapper to grant you full control over
manipulating output files
Hello Di,
The tool "Filter and Sort -> Select" can be used to select lines from a
.bed file for chr1 only. On the tool form, in text box labeled "the
pattern:", enter this term:
^chr1\s
Then sort with the tool "Sort" from the same tool group.
Hopefully this helps,
Best,
Jen
Galaxy team
O
Hello Clare,
An example of how to sort a SAM file is included in the workflow from #2
on this FAQ (it can be imported and the sort modified as needed):
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq
If you are starting with a BAM file, convert BAM->SAM, then after
sorting, back wi
Can anyone point me to a good workflow to convert my ChIP-seq data intervals to
gene names. My peaks fall both within genes and within intergenic areas.
Thanks,
Chris
Christopher Futtner, Ph.D.
Dept. of Surgery
Duke University
Durham, NC 27710
email: christopher.futt...@duke.edu
phone: 919-684-11
Hello,
There is no general workflow, primarily because there is no single
source of gene annotation and some formatting may be necessary. But once
that part is resolved, using a single tool in "Operate on Genomic
Intervals" can most often assign gene names to query genome regions.
The first
Hello Sheena,
It is odd that this particular genome exists in two versions, with
different content, for the same release number/date. Ensemble will
update annotation with new releases, but not the reference genome itself
unless they also increment the genome build number.
The Zebrafish proje
Good Afternoon Sheena:
Can you please explain what is different between the Ensembl and UCSC
Zebrafish Zv9 genome sequences ?
--Hiram
On 11/4/11 2:50 PM, Scroggins, Sheena wrote:
How do I upload the Zebrafish genome from Ensembl to my user history
in Galaxy? I'm trying to map my RNA-Seq data
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