Hi Prash,
You have reach the galaxy-u...@bx.psu.edu mailing list that supports the
public Galaxy instance at http://usegalaxy.org. Sometimes we can help
with broader questions, but for general bioinformatics help I would
search, then ask, the communities at a web sites such as biostars.org
and seqanswers.com. The original tool author and any web sites they
support are also good resources.
That said, to give some short help for your questions (but follow up
with the above):
1 - most any short read dataset can be run with blast - so I am not
sure what you are asking. when you ask at the other sites, add more
details about your goal.
2 - running a tool such as FastQC can give you an idea about sequence
quality (if that is what you mean by "better"). some tools require
paired end data, so that could make it automatically better. If you are
wondering which set is contributing in a "better" way to the assembly,
then asking other users of the tool, ideally working with a similar
genome, how they determine this would be a good place to start.
3 - to annotate assembly results with chromosome assignment - how to do
this depends on what other data is available for your genome (genomic or
transcripts/genes). Or what related genomes may be available
(comparative). The basic idea would be to compare against known to make
assignments.
There is a repository for this tool in the Galaxy Tool Shed, for use to
local or cloud instances, but it sounds like you already saw that.
http://usegalaxy.org/toolshed. If you had technical problems with that
tool, the tool author could be contacted. Although if the tool fails on
the line command, then there is likely a bigger issue as you suspect
(memory or otherwise), and the wrapper would be unlikely to change that.
But, you could also move to a cloud instance with more resource.
http://usegalaxy.org/cloud
Good luck!
Jen
Galaxy team
On 12/16/13 2:14 AM, Prash wrote:
Dear All
Greetings! I am analysing a genome of ca. 3.4Mb where I have paired.fa
and unpaired.fa files as of now. The sequences have been trimmed
before that. Now when I assemble these reads using 'ssake -f paired
-g unpaired ...', it takes hell lot of time. Perhaps, I am running
out of memory in analyzing the sequence reads. I could use galaxy
platform, but would like to stick with ssake.
Few questions:
What if I concatenate these two files, would I be able to peruse this
for blasting against my reference?
At this point, how do I know whether or not paired or single-end reads
are better?
How do I know the two chromosomal sequences?
Help appreciated for stupid questions :)
Thank you in advance
Prash
Prashanth Suravajhala, PhD.
Homepage: http://www.bioinformatics.org/wiki/Prash
<http://www.bioinformatics.org/wiki/Prash>
Linkedin: http://dk.linkedin.com/in/prashbio
<http://dk.linkedin.com/in/prashbio>
"What counts in life is not the mere fact that we have lived. It is
what difference we have made to the lives of others that will
determine the significance of the life we lead." --- Nelson Mandela
On 15 December 2013 18:00, <galaxy-user-requ...@lists.bx.psu.edu
<mailto:galaxy-user-requ...@lists.bx.psu.edu>> wrote:
Send galaxy-user mailing list submissions to
galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.bx.psu.edu/listinfo/galaxy-user
or, via email, send a message with subject or body 'help' to
galaxy-user-requ...@lists.bx.psu.edu
<mailto:galaxy-user-requ...@lists.bx.psu.edu>
You can reach the person managing the list at
galaxy-user-ow...@lists.bx.psu.edu
<mailto:galaxy-user-ow...@lists.bx.psu.edu>
When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-user digest..."
HEY! This is important! If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-user Digest
Vol ..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the
thread you are responding to.
Why?
1. This will keep the subject meaningful. People will have some
idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that
match search queries, but that aren't actually informative.
Today's Topics:
1. Re: fastqc and blast? trinity? (Peter Cock)
----------------------------------------------------------------------
Message: 1
Date: Sat, 14 Dec 2013 21:18:29 +0000
From: Peter Cock <p.j.a.c...@googlemail.com
<mailto:p.j.a.c...@googlemail.com>>
To: Jorge Braun <braun_...@hotmail.com <mailto:braun_...@hotmail.com>>
Cc: "galaxy-user@lists.bx.psu.edu
<mailto:galaxy-user@lists.bx.psu.edu>"
<galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>>
Subject: Re: [galaxy-user] fastqc and blast? trinity?
Message-ID:
<CAKVJ-_4BKUgtb37EYF_FsAAj=yc+et5zurvfgzk0puyskdm...@mail.gmail.com <mailto:yc%2bet5zurvfgzk0puyskdm...@mail.gmail.com>>
Content-Type: text/plain; charset=ISO-8859-1
On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun
<braun_...@hotmail.com <mailto:braun_...@hotmail.com>> wrote:
>
> Hello, of course, Jennifer is right for the first question . For
> the second question about blast ... I wonder if running after
> blast in galaxy I can remove sequences that can contaminate
> the data. It's possible?
>
The BLAST suite is not available on the public Galaxy
server at http://usegalaxy.org but is available from the
Galaxy Tool Shed if you have a local Galaxy instance:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
One way to filter your FASTA file based on BLAST hits
would be to use the tabular output from BLAST with
this sequence filtering tool:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
e.g. If you want to remove transcripts which seem
to be mitochondria, you could BLAST against a
mitochondrial database, and take only the sequence
with no hits.
Regards,
Peter
------------------------------
_______________________________________________
galaxy-user mailing list
galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>
http://lists.bx.psu.edu/listinfo/galaxy-user
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
End of galaxy-user Digest, Vol 90, Issue 13
*******************************************
___________________________________________________________
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
