Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics
Thanks Ross, I don't see it under my local install - are there any pre-written scripts to integrate it with a local galaxy instance? I assume you are talking about this tool here: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ -John From: Ross [ross.laza...@gmail.com] Sent: Wednesday, June 01, 2011 11:41 AM To: John David Osborne Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics You can avoid the space/time overhead of grooming and get comprehensive QC reports using the new wrapper for FastQC (under NGS: QC) - it takes fastq of any flavour (and bam) groomed or not, producing a superset of the compute quality stats output without the need for an intermediate step. Highly recommended. On Wed, Jun 1, 2011 at 12:02 PM, John David Osborne ozb...@uab.edu wrote: I noticed that for our new Ilumina data (which generate Sanger format) the FastQ groomer output is identical to the Ilumina FastQ input file. I was hoping to go ahead and just use the raw FastQ files as input (saving disk space) for computing quality statistics to look at box plots, but it appears that the tool Compute Quality Statistics appears to require that the data have been run through FastQ Groomer first. Is there a way to get around this and is this a bug? I assuming this is some sort of safety measure built into this tool? -John ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics
On Thu, Jun 9, 2011 at 10:12 AM, John David Osborne ozb...@uab.edu wrote:
Thanks Ross, I don't see it under my local install - are there any
pre-written scripts to integrate it with a local galaxy instance?
I assume you are talking about this tool here:
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
Hi, John.
it's on main and test - ie the FastQC wrapper is distributed with the
current stable and central branches so your local tool_conf.xml may be
out of date since it's not automagically refreshed from the distro
.sample ? If you do a diff of your local tool_conf.xml with the
current distributed sample, you should see the lines you need to add
which points to rgenetics/fastqc.xml
Thu,Jun 09 at 10:22am grep -i fastqc tool_conf.xml
label text=FastQC: fastq/sam/bam id=fastqcsambam /
tool file=rgenetics/rgFastQC.xml /
Like everything else, you'll want to install the jar locally so it can
be found by the cluster - the default location is
tool-data/shared/jars/FastQC so the tool can find the fastqc perl
script (yes, I know...but it's worth it!)
command interpreter=python
rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file
-n $out_prefix -f $input_file.ext -e
${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc
I hope this helps?
-John
From: Ross [ross.laza...@gmail.com]
Sent: Wednesday, June 01, 2011 11:41 AM
To: John David Osborne
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics
You can avoid the space/time overhead of grooming and get
comprehensive QC reports using the new wrapper for FastQC (under NGS:
QC) - it takes fastq of any flavour (and bam) groomed or not,
producing a superset of the compute quality stats output without the
need for an intermediate step. Highly recommended.
On Wed, Jun 1, 2011 at 12:02 PM, John David Osborne ozb...@uab.edu wrote:
I noticed that for our new Ilumina data (which generate Sanger format) the
FastQ groomer output is identical to the Ilumina FastQ input file.
I was hoping to go ahead and just use the raw FastQ files as input (saving
disk space) for computing quality statistics to look at box plots, but it
appears that the tool Compute Quality Statistics appears to require that
the data have been run through FastQ Groomer first.
Is there a way to get around this and is this a bug? I assuming this is some
sort of safety measure built into this tool?
-John
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics
You can avoid the space/time overhead of grooming and get comprehensive QC reports using the new wrapper for FastQC (under NGS: QC) - it takes fastq of any flavour (and bam) groomed or not, producing a superset of the compute quality stats output without the need for an intermediate step. Highly recommended. On Wed, Jun 1, 2011 at 12:02 PM, John David Osborne ozb...@uab.edu wrote: I noticed that for our new Ilumina data (which generate Sanger format) the FastQ groomer output is identical to the Ilumina FastQ input file. I was hoping to go ahead and just use the raw FastQ files as input (saving disk space) for computing quality statistics to look at box plots, but it appears that the tool Compute Quality Statistics appears to require that the data have been run through FastQ Groomer first. Is there a way to get around this and is this a bug? I assuming this is some sort of safety measure built into this tool? -John ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
