Error introduced with Fastq Groomer
Hi, Some unexpected symbols were introduced while grooming my fastq file Before @DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACGTCTGCATTACACGCTTCATTAGGGACTTCCC + @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C< After @DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACG+1�CATTACACGCTTCATTAGGGACTTCCC + @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C< I relaunch this step without being able to reproduce the bug. Any ideas about this problem ? Have you guys came across the same problem before ? Regards, Philip
Hi Philippe, I’m unable to suggest a reason as to why this has happened, other than some sort of corruption whilst the job was running, but I would point out two things to you. 1. I don’t think you need to run the fastq groomer on your data anyway as it’s in Illumina 1.8+ format, which should already be in fastqsanger format. 2. It appears that the fastq groomer hasn’t worked as the quality scores haven’t changed format. (A general question to anyone here – will fastq groomer change the quality format of reads that are already in fastqsanger format?) Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 From: Philippe Moncuquet <philippe.mcqt@gmail.com<mailto:philippe.mcqt@gmail.com>> Date: Monday, 10 February 2014 03:50 To: Galaxy Dev <galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>> Subject: [galaxy-dev] Error introduced with Fastq Groomer Hi, Some unexpected symbols were introduced while grooming my fastq file Before @DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACGTCTGCATTACACGCTTCATTAGGGACTTCCC + @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C< After @DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACG+1�CATTACACGCTTCATTAGGGACTTCCC + @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C< I relaunch this step without being able to reproduce the bug. Any ideas about this problem ? Have you guys came across the same problem before ? Regards, Philip
The groomer was recently migrated to the tool shed - this has not been released as part of a galaxy-dist though so I assume you are still running a version of the fastq groomer bundled with Galaxy? If yes, what version of Galaxy are you running (i.e. can you attach the output of "hg summary")? -John On Mon, Feb 10, 2014 at 7:00 AM, graham etherington (TSL) <graham.etherington@sainsbury-laboratory.ac.uk> wrote:
Hi Philippe, I’m unable to suggest a reason as to why this has happened, other than some sort of corruption whilst the job was running, but I would point out two things to you.
1. I don’t think you need to run the fastq groomer on your data anyway as it’s in Illumina 1.8+ format, which should already be in fastqsanger format. 2. It appears that the fastq groomer hasn’t worked as the quality scores haven’t changed format. (A general question to anyone here – will fastq groomer change the quality format of reads that are already in fastqsanger format?)
Cheers, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
From: Philippe Moncuquet <philippe.mcqt@gmail.com> Date: Monday, 10 February 2014 03:50 To: Galaxy Dev <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Error introduced with Fastq Groomer
Hi,
Some unexpected symbols were introduced while grooming my fastq file
Before
@DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACGTCTGCATTACACGCTTCATTAGGGACTTCCC + @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C<
After
@DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACG+1�CATTACACGCTTCATTAGGGACTTCCC + @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C<
I relaunch this step without being able to reproduce the bug. Any ideas about this problem ? Have you guys came across the same problem before ?
Regards,
Philip
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participants (3)
-
graham etherington (TSL) -
John Chilton -
Philippe Moncuquet