Hi,
I would like to extract raw counts from tophat output. Does anyone know a
way to do this in Galaxy?
Thanks!
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Hello,
I am getting what seems to me to be strange results using two different
mapping tools in Galaxy. I am mapping illumina RNA-seq data and with
tophat, while setting # alignments to 1, I get around 15-20% reads mapping.
And when I use bwa, I am getting around 75% reads mapping. My reference
- On *Wed, 4/27/11, Austin Paul * wrote:
>
>
> From: Austin Paul
> Subject: [galaxy-user] mapping with tophat vs. bwa
> To: galaxy-user@lists.bx.psu.edu
> Date: Wednesday, April 27, 2011, 4:20 PM
>
>
> Hello,
>
> I am getting what seems to me to be strange results u
Hi,
You need to run fastq groomer on your rna-seq data. Your reference is fine
as a fasta.
Austin
On Fri, May 6, 2011 at 10:26 AM, wrote:
>
> Hi David,
>
> Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and
> it says "History does not include a dataset of the required f
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 reference and the sam file, then use IGVtools to index the sam
file, then I can visualize the data.
Austin
On Fri, May 6, 2011 at 5:30 PM,
Oops. Good to know. Thanks.
Austin
On Fri, May 6, 2011 at 6:02 PM, Sean Davis wrote:
> 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. I
===> Please use "Reply All" when responding to this email! <===
Hello,
I am curious if the line estimation shown in the history window for pileup
generation is at all accurate. I am using the pileup files to generate
expression data from bwa mapping for looking at differential expression, but
I
e history with
> me and I'll take a look to see what happened with those particular datasets.
>
> Thanks!
>
> -Dannon
>
> On Aug 25, 2011, at 6:08 PM, Austin Paul wrote:
>
> > ===> Please use "Reply All" when responding to this email! <===
>
Hello,
I recently figured out how to filter the output bwa SAM file for flag type
in order to determine the number of reads that were successfully mapped. My
question is, I previously thought I could generate a pileup, then sum the
number of counts for each base of the reference, and divide this
, Austin Paul wrote:
> Hello,
>
> I recently figured out how to filter the output bwa SAM file for flag type
> in order to determine the number of reads that were successfully mapped. My
> question is, I previously thought I could generate a pileup, then sum the
> number of counts fo
You could try "fasta width formatter" on your reference fasta. This has
helped me in the past when I received a similar error.
On Tue, Sep 13, 2011 at 11:32 AM, Zachary A Lewis wrote:
> Hi,
> I was wondering if someone could help me with an error message I'm getting
> after performing a sam to
Hi Zach,
You should reply to all so people dont keep working on your questions. Glad
to help.
Austin
-- Forwarded message --
From: Zachary A Lewis
Date: Tue, Sep 13, 2011 at 3:10 PM
Subject: Re: [galaxy-user] Help with sam to bam
To: Austin Paul
Thanks Austin! That did the
Hi,
I am curious if anyone knows how to select random lines from a fastq file.
There is a select random lines tool in text manipulation tools, but it does
not treat fastq files specifically, so it will not group quality lines with
sequence lines. And if I turn the fastq file to tabular form in or
interested in?
Austin
On Tue, Nov 8, 2011 at 2:07 PM, Peter Cock wrote:
> On Tue, Nov 8, 2011 at 9:57 PM, Austin Paul wrote:
> > Hi,
> >
> > I am curious if anyone knows how to select random lines from a fastq
> file.
> > There is a select random lines tool in t
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