Hello Galaxy users,

Just to follow-up on my user group question described in the list-serv e-mail 
just sent out.

I put forth the question about FASTQ collapse, as the FASTX-toolkit by Assaf 
Gordon describes the supported collapse tool as follows:

"FASTQ/A Collapser, Collapsing identical sequences in a FASTQ/A file into a 
single sequence (while maintaining reads counts)"

Yet, the collapse tool in Galaxy appears to be FASTA supported only?

Why am I asking?

Would like to remove duplicate reads in a FASTQ file by sequence, leaving one 
representative unique read having the best quality line among the duplicates it 
was identified from.

Can certainly convert FASTQ to FASTA, then collapse, but if you do not have the 
qual file, you cannot reconstitute a FASTQ file with actual qual scores.

Any argument for or against?  Or can Galaxy already do and I am missing the 
tool to actually use?

Thanks ... best,

Kory

--------------------------------------------

Kory R. Johnson, MS, PhD
Sr. Bioinformatics Scientist



www.kellygovernmentsolutions.com

Providing Contract Services For:

Bioinformatics Section,
Information Technology & Bioinformatics Program,
Division of Intramural Research (DIR),
National Institute of Neurological Disorders & Stroke (NINDS),
National Institutes of Health (NIH),
Bethesda, Maryland

Mailing Address:

NINDS/NIH
Clinical Center (Building 10)
Office 5S223
9000 Rockville Pike
Bethesda, MD 20892

Contact Information:

Phone:    301-402-1956
Fax:           301-480-3563
email:       johnso...@ninds.nih.gov

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you.

--------------------------------------------

-----Original Message-----
From: galaxy-user-requ...@lists.bx.psu.edu 
[mailto:galaxy-user-requ...@lists.bx.psu.edu]
Sent: Thursday, February 03, 2011 12:52 PM
To: galaxy-user@lists.bx.psu.edu
Subject: galaxy-user Digest, Vol 56, Issue 4

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Today's Topics:

   1. CuffDiff gene fpkm tracking file. (Samuele Gherardi)
   2. CuffDiff gene fpkm tracking file- Sorry! I sent only a part
      of my email (Samuele Gherardi)
   3. Re: listing attributes of data input (Peter)
   4. Re: CuffDiff gene fpkm tracking file. (Jeremy Goecks)
   5. Re: Downloadable Galaxy Virtual Machine in VMware
      (Haarst, Jan van)
   6. Re: Downloadable Galaxy Virtual Machine in VMware (Nate Coraor)
   7. FASTQ collapse? (Johnson, Kory (NIH/NINDS) [C])


----------------------------------------------------------------------

Message: 1
Date: Thu, 3 Feb 2011 09:53:44 +0000
From: Samuele Gherardi <samuele.ghera...@unibo.it>
To: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] CuffDiff gene fpkm tracking file.
Message-ID:
        
<025db19130de0b43bbd868bdb9244a82c...@e10-mbx3-dr.personale.dir.unibo.it>

Content-Type: text/plain; charset="iso-8859-1"



this is an example of my CuffDiff gene fpkm tracking file.

tracking_id     class_code      nearest_ref_id  gene_short_name tss_id  locus   
q1_FPKM q1_conf_lo      q1_conf_hi      q2_FPKM q2_conf_lo      q2_conf_hi
XLOC_000001     -       -       MT-ND5  -       chrM:0-16571    12484.2 12260.8 
12707.7 11447   11233.1 11661
XLOC_000002     -       -       USP14   TSS1,TSS2,TSS3  chr18:148586-236453     
16.7235 9.41244 24.0346 19.437  11.7368 27.1371
XLOC_000003     -       -       SMCHD1  
TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540   28.2493 
17.5093 38.9892 27.2263 16.6263 37.8262
XLOC_000004     -       -       EMILIN2 TSS13,TSS14     chr18:2880607-2882469   
3.98118 0       7.99721 4.62875 0.278519        8.97899

I this is normal, how can I find the class code of transcript listed in the 
CuffDiff gene expression file?


thank you in advance

Samuele.



------------------------------

Message: 2
Date: Thu, 3 Feb 2011 10:58:47 +0000
From: Samuele Gherardi <samuele.ghera...@unibo.it>
To: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] CuffDiff gene fpkm tracking file- Sorry! I sent
        only a part of my email
Message-ID:
        
<025db19130de0b43bbd868bdb9244a82c...@e10-mbx3-dr.personale.dir.unibo.it>

Content-Type: text/plain; charset="iso-8859-1"

Hello everybody,
I'm quite new in NGS world, I'm trying to analize dome RNA-seq data. I followed 
the workflow through tophat,cufflink,cuffcompare and cuffdiff
I suppose everything work fine but in the  Cuffdiff gene fpkm file the column 
Class_Code is empty and i don't know why?

this is an example of my CuffDiff gene fpkm tracking file.

tracking_id     class_code      nearest_ref_id  gene_short_name tss_id  locus   
q1_FPKM q1_conf_lo      q1_conf_hi      q2_FPKM q2_conf_lo      q2_conf_hi
XLOC_000001     -       -       MT-ND5  -       chrM:0-16571    12484.2 12260.8 
12707.7 11447   11233.1 11661
XLOC_000002     -       -       USP14   TSS1,TSS2,TSS3  chr18:148586-236453     
16.7235 9.41244 24.0346 19.437  11.7368 27.1371
XLOC_000003     -       -       SMCHD1  
TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540   28.2493 
17.5093 38.9892 27.2263 16.6263 37.8262
XLOC_000004     -       -       EMILIN2 TSS13,TSS14     chr18:2880607-2882469   
3.98118 0       7.99721 4.62875 0.278519        8.97899

I this is normal, how can I find the class code of transcript listed in the 
CuffDiff gene expression file?


thank you in advance

Samuele.



------------------------------

Message: 3
Date: Thu, 3 Feb 2011 11:05:07 +0000
From: Peter <pe...@maubp.freeserve.co.uk>
To: Freddy de Bree <freddy.deb...@wur.nl>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] listing attributes of data input
Message-ID:
        <aanlktimkxwr_9mfudu7ws+qaphtfrqdj+rrukrlts...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Thu, Feb 3, 2011 at 8:40 AM, Freddy de Bree <freddy.deb...@wur.nl> wrote:
> Dear all,
>
> I was wondering if there is a place within the Galaxy content (a config, an
> xml file)
> that gives me some handles on how to address attributes of data input.
>
> For example, I can get the 'file_name' of data input, by addressing this
> attr
> as 'input.file_name', and for example, the original name of the data file
> can be addressed with 'input.name'.
>
> Anyone any clues where I can find this info?
>
> Freddy de Bree

Some are given in examples on the main tool XML doc page,
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax

Others I've noticed by looking at the provided XML wrappers,
and/or email list questions. For example, .ext or .extension gives
the Galaxy file type (e.g. fasta).

Other than that, I guess you can always read the code - but I
agree that a document describing this would be nice to have.

Peter


------------------------------

Message: 4
Date: Thu, 3 Feb 2011 09:14:19 -0500
From: Jeremy Goecks <jeremy.goe...@emory.edu>
To: Samuele Gherardi <samuele.ghera...@unibo.it>
Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] CuffDiff gene fpkm tracking file.
Message-ID: <b60dbe14-31bd-432d-92bb-fb7c8363a...@emory.edu>
Content-Type: text/plain; charset=us-ascii

>
> this is an example of my CuffDiff gene fpkm tracking file.
>
> tracking_id     class_code      nearest_ref_id  gene_short_name tss_id  locus 
>   q1_FPKM q1_conf_lo      q1_conf_hi      q2_FPKM q2_conf_lo      q2_conf_hi
> XLOC_000001     -       -       MT-ND5  -       chrM:0-16571    12484.2 
> 12260.8 12707.7 11447   11233.1 11661
> XLOC_000002     -       -       USP14   TSS1,TSS2,TSS3  chr18:148586-236453   
>   16.7235 9.41244 24.0346 19.437  11.7368 27.1371
> XLOC_000003     -       -       SMCHD1  
> TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540   
> 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262
> XLOC_000004     -       -       EMILIN2 TSS13,TSS14     chr18:2880607-2882469 
>   3.98118 0       7.99721 4.62875 0.278519        8.97899
>
> I this is normal, how can I find the class code of transcript listed in the 
> CuffDiff gene expression file?
>


Hi Samuele,

Without seeing your history, it's difficult to say for certain what your 
problem is. However, I'd guess that the GTF file that you're providing to 
Cuffdiff does not have the p_id attribute. You can produce a GTF file with both 
tss_id and p_id attributes by running Cuffcompare and using sequence data.

Thanks,
J.


------------------------------

Message: 5
Date: Thu, 3 Feb 2011 16:54:14 +0100
From: "Haarst, Jan van" <jan.vanhaa...@wur.nl>
To: "'Leon Mei'" <hailiang....@nbic.nl>,
        "'galaxy-user@lists.bx.psu.edu'"        <galaxy-user@lists.bx.psu.edu>
Cc: 'David van Enckevort' <david.van.enckev...@nbic.nl>,        'Rob Hooft'
        <rob.ho...@nbic.nl>
Subject: Re: [galaxy-user] Downloadable Galaxy Virtual Machine in
        VMware
Message-ID:
        <48b2c6e110f6cc4387afcd2ebcca0b3b25d12d4...@scomp0536.wurnet.nl>
Content-Type: text/plain; charset="iso-8859-1"

The download can also be done using bittorrent, torrent is available at 
http://www.biotorrents.net/details.php?id=136 .
This might be faster, as one of the peers is in Canada.

With kind regards,
Jan


> -----Original Message-----
> From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-
> boun...@lists.bx.psu.edu] On Behalf Of Leon Mei
> Sent: Tuesday, February 01, 2011 1:08 PM
> To: galaxy-user@lists.bx.psu.edu
> Cc: David van Enckevort; Rob Hooft
> Subject: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware
>
> Dear list,
>
> Within the Netherlands Bioinformatics Centre, we have implemented a Galaxy VM 
> by
> wrapping up the distributed version from PennState. We are also adding more 
> easy-to-
> use pipelines for Genomics and Proteomics data analysis into this server at 
> the
> moment.
>
> You can download the current version at: http://bet1.nbiceng.net/galaxy/
>
> More documents can be found at: https://wiki.nbic.nl/index.php/Galaxy_VM
>
> By sharing this VM, we hope to relieve you from the normal installation and
> configuration steps (sometimes can be difficult) if you want to run a local 
> Galaxy
> instance.
>
> If you are interested in this procedure or have questions on that, we are 
> happy to
> share our experience and scripts.
>
> Best regards,
> Leon
>
> --
> Hailiang (Leon) Mei
> Netherlands Bioinformatics Center (http://www.nbic.nl/)
> Skype: leon_mei? ? Mobile: +31 6 41709231
>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user





------------------------------

Message: 6
Date: Thu, 3 Feb 2011 11:37:01 -0500
From: Nate Coraor <n...@bx.psu.edu>
To: "Haarst, Jan van" <jan.vanhaa...@wur.nl>
Cc: "'galaxy-user@lists.bx.psu.edu'" <galaxy-user@lists.bx.psu.edu>,
        'Leon Mei' <hailiang....@nbic.nl>,      'David van Enckevort'
        <david.van.enckev...@nbic.nl>,  'Rob Hooft' <rob.ho...@nbic.nl>
Subject: Re: [galaxy-user] Downloadable Galaxy Virtual Machine in
        VMware
Message-ID: <20110203163701.ge15...@bx.psu.edu>
Content-Type: text/plain; charset=iso-8859-1

Haarst, Jan van wrote:
> The download can also be done using bittorrent, torrent is available at 
> http://www.biotorrents.net/details.php?id=136 .
> This might be faster, as one of the peers is in Canada.

This is great!  I haven't checked the image out, but I'm fetching the
torrent now and will leave it seeding here from PSU to help out.

Thanks,
--nate

>
> With kind regards,
> Jan
>
>
> > -----Original Message-----
> > From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-
> > boun...@lists.bx.psu.edu] On Behalf Of Leon Mei
> > Sent: Tuesday, February 01, 2011 1:08 PM
> > To: galaxy-user@lists.bx.psu.edu
> > Cc: David van Enckevort; Rob Hooft
> > Subject: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware
> >
> > Dear list,
> >
> > Within the Netherlands Bioinformatics Centre, we have implemented a Galaxy 
> > VM by
> > wrapping up the distributed version from PennState. We are also adding more 
> > easy-to-
> > use pipelines for Genomics and Proteomics data analysis into this server at 
> > the
> > moment.
> >
> > You can download the current version at: http://bet1.nbiceng.net/galaxy/
> >
> > More documents can be found at: https://wiki.nbic.nl/index.php/Galaxy_VM
> >
> > By sharing this VM, we hope to relieve you from the normal installation and
> > configuration steps (sometimes can be difficult) if you want to run a local 
> > Galaxy
> > instance.
> >
> > If you are interested in this procedure or have questions on that, we are 
> > happy to
> > share our experience and scripts.
> >
> > Best regards,
> > Leon
> >
> > --
> > Hailiang (Leon) Mei
> > Netherlands Bioinformatics Center (http://www.nbic.nl/)
> > Skype: leon_mei? ? Mobile: +31 6 41709231
> >
> > _______________________________________________
> > galaxy-user mailing list
> > galaxy-user@lists.bx.psu.edu
> > http://lists.bx.psu.edu/listinfo/galaxy-user
>
>
>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
>


------------------------------

Message: 7
Date: Thu, 3 Feb 2011 12:51:34 -0500
From: "Johnson, Kory (NIH/NINDS) [C]" <johnso...@ninds.nih.gov>
To: "'galaxy-u...@bx.psu.edu'" <galaxy-u...@bx.psu.edu>
Subject: [galaxy-user] FASTQ collapse?
Message-ID:
        <f142c51c02c33c418e931103600d1e670648e93...@nihmlbxbb03.nih.gov>
Content-Type: text/plain; charset="us-ascii"

Hello,

Is there an option to collapse duplicate sequences in FASTQ format.

I see collapse for FASTA, but where is it for FASTQ?

Thank you,

Kory

--------------------------------------------

Kory R. Johnson, MS, PhD
Sr. Bioinformatics Scientist

[cid:image001.jpg@01CBC39E.D7F751F0]

www.kellygovernmentsolutions.com

Providing Contract Services For:

Bioinformatics Section,
Information Technology & Bioinformatics Program,
Division of Intramural Research (DIR),
National Institute of Neurological Disorders & Stroke (NINDS),
National Institutes of Health (NIH),
Bethesda, Maryland

Mailing Address:

NINDS/NIH
Clinical Center (Building 10)
Office 5S223
9000 Rockville Pike
Bethesda, MD 20892

Contact Information:

Phone:    301-402-1956
Fax:           301-480-3563
email:       johnso...@ninds.nih.gov

P Green Message:

Please consider the environment before printing this e-mail.  Thank you.

Important Message:

This electronic message transmission contains information intended for the 
recipient only.  Such that, the information contained herein may be 
confidential, privaledged, or proprietary.  If you are not the intended 
recipient, be aware that any disclosure, copying, distribution, or use of this 
information is strictly prohibited.  If you have received this electronic 
information in error, please notify the sender immediately by telephone.  Thank 
you.

--------------------------------------------

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