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   
Linkedin: 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-request@lists.bx.psu.edu> wrote:
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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.cock@googlemail.com>
To: Jorge Braun <braun_bio@hotmail.com>
Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] fastqc and blast? trinity?
Message-ID:
        <CAKVJ-_4BKUgtb37EYF_FsAAj=YC+eT5ZuRvFgZk0pUySKdmsxg@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun <braun_bio@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


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