Re: [galaxy-user] Assembly of Paired and Unpaired sequences

2013-12-16 Thread Prash 
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


“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  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 
> 
>
> “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,  wrote:
>
>> Send galaxy-user mailing list submissions to
>> galaxy-user@lists.bx.psu.edu
>>
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>>
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>>
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>> 1. Change the subject of your response from "Galaxy-user Digest Vol ..."
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>> 2. Strip out everything else in the digest that is not part of the thread
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>>
>> Why?
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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 +
>> From: Peter

Re: [galaxy-user] Assembly of Paired and Unpaired sequences

2013-12-16 Thread Jennifer Jackson 

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 



"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, > wrote:


Send galaxy-user mailing list submissions to
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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 +
From: Peter Cock mailto:p.j.a.c...@googlemail.com>>
To: Jorge Braun mailto:braun_...@hotmail.com>>
Cc: "galaxy-user@lists.bx.psu.edu
"
mailto:galaxy-user@lists.bx.psu.edu>>
Subject: Re: [galaxy-user] fastqc and blast? trinity?
Message-ID:
   
mailto:yc%2bet5zurvfgzk0puyskdm...@mail.gmail.com>>

Content-Type: tex

[galaxy-user] Assembly of Paired and Unpaired sequences

2013-12-16 Thread Prash 
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,  wrote:

> Send galaxy-user mailing list submissions to
> 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
>
> You can reach the person managing the list at
> 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 +
> From: Peter Cock 
> To: Jorge Braun 
> Cc: "galaxy-user@lists.bx.psu.edu" 
> Subject: Re: [galaxy-user] fastqc and blast? trinity?
> Message-ID:
>  yc+et5zurvfgzk0puyskdm...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun 
> 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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