Lishiyong,
You should not convert colorspace to base space prior to aligning reads.
The reason for this is that if there is an error in one of the color
calls, it will effect all the downstream color calls.
Instead, you should use an aligner that will do the assembly in
color-space instead.
Jo,
Use the SAM Tools SAM-TO-BAM tool in Galaxy to convert your SAM file to
a BAM file.
Ryan
On 3/25/11 10:35 AM, Jochen Seggewiß wrote:
Hi!
Thank you for your reply.
So that means, I should convert the csfasta & qual to fastq, map it with
Bowtie, get an SAM, convert it to BAM and then in
I'm analyzing a bunch of datasets in a single history and the number of
history items is getting a little confusing. Is it possible to attached
a label a group of history items, or collapse a group of history items
on the display?
I don't suppose it is, but it would be a nice feature...
--
Hi - Has anyone developed a gene fusion detection workflow in Galaxy
that they would care to share?
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Plea
Cufflinks requires an 'xs' tag on each read in the bam file. Only tophat does
this. You can write a script to add this or remap with tophat.
How much of a difference do you see between tophat and bioscope?
Please excuse any typos -- Sent from my iPhone
On Apr 11, 2011, at 9:46 AM, lishiyong w
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