because the ending bases are the same.
Does this mean that I need to modified the coordinates first and then use
the Fetch Sequences to get the correct sequence? I thought UCSC and galaxy
were both 0 base?
Thanks.
Sean
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n stored in the file database?
Thanks,
Sean
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The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances and the Galaxy source code, p
On Thu, Feb 17, 2011 at 5:48 AM, Peter Cock wrote:
> On Thu, Feb 17, 2011 at 3:00 AM, Sean Davis wrote:
> > I have a tool that takes a pdb file as input. The authors of the
> *compiled*
> > code require that the suffix be either ".pdb" or ".ent". When
.
Sean
On Tue, Apr 5, 2011 at 12:31 PM, Slim Sassi wrote:
> Hello,
> I tried to use NGS: SAM Tools ->flagstat on a BAM files for basic stats, but
> I got results like you see below. It doesn't seem to be working. Any
> suggestions?
> 26584869 in total
>
> 0 QC failure
>
On Apr 5, 2011 1:05 PM, "Slim Sassi" wrote:
>
> Sean,
> You are correct, I did use tophat. Can you or anyone suggest a program
for BAM/SAM stats where the alignment was done with tophat
>
Slim,
What stats do you want to capture? The output you gave for flagstats is
On Tue, Apr 5, 2011 at 2:01 PM, Slim Sassi wrote:
> Sean,
> I only wanted to start collecting stats with flagstats but knew that I
> needed something else to get everthing needed.
> I would like to know:
> % that didn't pass QC
That information is not in the FASTQ files, so i
Hi, Mike. See my couple of comments below
Sean
On Tue, Apr 5, 2011 at 2:22 PM, Mike Dufault wrote:
> Hi all,
>
>
>
> Like many people on this e-mail chain, I have been looking for advice on
> how to process Exome data. Below, I have described in detail what I have
>
On Fri, Apr 8, 2011 at 7:42 AM, Mike Dufault wrote:
> Sean, Anton and Jen,
>
> Thanks for all of the suggestions (in separate replies) on how to better
> analyze my SelectSure captured Exome data. My original work-flow is below in
> the e-mail string.
>
> Based on the s
IGV reads BAM files just fine; no need to convert to SAM.
Sean
On Fri, May 6, 2011 at 8:45 PM, Austin Paul wrote:
> There are many ways. I typically use IGV. It needs a sam file, so I first
> convert the bam to sam in galaxy, then download the sam file. In IGV, I
> upload the refe
nformation from SRA is likely only an approximation. SRA does not
validate these details, I do not think.
You can probably use the distribution from your data as the best estimate.
Sean
Thanks.
>
> Jianguang Du
>
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rdless of the
technology used. In particular, one would never suggest running a
microarray experiment without replicates; one should follow
approximately the same rules for sequencing (and sequence data
analysis).
Sean
>>
>> Thanks,
>> ib
>
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