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 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:
- 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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End of galaxy-user Digest, Vol 90, Issue 13