On Oct 3, 2012, at 2:02 PM, Kshama Aswath wrote:
Hello:
I have this 20GB data that I have uploaded onto my history and trying to get
it run thr groomer. Just the first data set was uploaded yesterday and ran
groomer on it and it was not done this morning. The message indicated taht it
is
Matthew,
yes we have seen such kind of long runs before (depending on server load).
Happy most of our reads are now in 1.8+ format.
You can parallelise the process by splitting the file in 4 or 6 and submit for
grooming and afterwards merge them again...
Alex
Hello Slon,
In case you are still having issues, the best use case for Illumina 1.8+
data is to run the FASTQ Groomer tool with the option Sanger. As Peter
noted, this assigns the expected datatype plus verifies content before
investing time in downstream analysis.
Please let us know if
actually Illumina 1.8+ has one more quality value higher than fastqsanger
(see http://en.wikipedia.org/wiki/FASTQ_format )
my question now I guess is if I use fastqsanger would it break anything
when it encounters the 'J' in the qual values?
On Tue, Oct 18, 2011 at 5:10 PM, Peter Cock
On Tue, Nov 1, 2011 at 4:58 PM, Kevin Lam abou...@gmail.com wrote:
actually Illumina 1.8+ has one more quality value higher than fastqsanger
(see http://en.wikipedia.org/wiki/FASTQ_format )
my question now I guess is if I use fastqsanger would it break anything when
it encounters the 'J' in
If Illumina 1.8+ is already using the Sanger FASTQ encoding, the file should
be recognized by downstream applications, like Quality statistics computer,
quality filter etc. However, my file is not visible by those programs and
when I click on it, only uploaded fastq file is displayed, without
[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
$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
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
9 matches
Mail list logo
