Thank you Jennifer.  That was a big help :)

Regards
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 16 December 2013 18:19, Jennifer Jackson <j...@bx.psu.edu> wrote:

>  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
> 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> wrote:
>
>> Send galaxy-user mailing list submissions to
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>> Today's Topics:
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>>    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>
>> To: Jorge Braun <braun_...@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+et5zurvfgzk0puyskdm...@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>
>> 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
>> *******************************************
>>
>
>
>
> ___________________________________________________________
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> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
___________________________________________________________
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