Hello Thomas,
Using Tophat would be fine. To understand the parameters used, click on
the "i" icon in the job run's dataset box in the history. For certain
tools, this is also captured (line command) in the "Info:" field after
the job completes.
Take care,
Jen
Galaxy team
On 8/9/11 1:28 AM, Thomas Jenner Pulikotial Augustine wrote:
Hi,
I would like to know whether i should use Tophat or LASTZ for
transcriptome analysis, the reads(transcriptome) were obtain from 454 GS
flx sequencer. Kindly reply, in the FAQ section we're suggested to use
Tophat but this was designed for Illumina genome analyzer. Thanks in
advance.
Br,
Thomas
On Mon, Aug 8, 2011 at 1:40 PM, Thomas Jenner Pulikotial Augustine
<[email protected] <mailto:[email protected]>> wrote:
Hi,
I would like to know the default options used by Galaxy to align 454
reads to reference genome using LASTZ alignment software. I'm trying
to align the query to a reference genome, kindly tell the me list of
options used for aligning the reads to reference genome. An
additional question, does Galaxy share scripts? i can across a link
that seems to be sharing scripts.
Br,
Thomas
On Sat, Jul 30, 2011 at 1:44 AM, Jennifer Jackson <[email protected]
<mailto:[email protected]>> wrote:
Hello Thomas,
For 454 data, there is a specific screencast that may be of
interest. Go to http://usegalaxy.org and scroll in the middle
pane to find quickie #15.
We have had very high usage over the last few days, but have
since been able to clear out more resource. Your job will likely
start within the next 24 hrs.
Hopefully this helps,
Thank you!
Jen
Galaxy team
On 7/29/11 4:18 AM, Thomas Jenner Pulikotial Augustine wrote:
Hi,
I'm trying to map a data set containing 454 reads to a
reference genome
using LASTZ alignment package in Galaxy. I'm following a
workflow used
for Illumina reads with the only change in the alignment
package, i'm
using LASTZ instead of bowtie/bwa. The following is the
procedure please
correct me if it's wrong and do suggest any additional
procedure to make
the workflow better.
In addition to this i'm, trying to do metagenomics analysis
as well
by following the procedure given in one of the video
tutorials. I've
submitted the files for alignment and its been a day since the
submission and the process has not yet started, could you
tell me what
could be the reason. The file size is 110Mb, under history
the package
indicate "Job is waiting run" how long does it usually take
to initiate
the process in the queue. Your suggestion's are valuable,
thanks for
developing Galaxy.
Kindly help, thank you.
1.Uploaded a FASTA file as input
2.Align using LASTZ
3.Filtering SAM files on bit-wise flag values
4.Finding how many reads are mapped to each chromosome
5.Sort the read counts
6.convert sam to bam
7.perform flagstat operation
Br,
Thomas
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http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
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