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Question: Need help with "FASTQ Groomer" tool
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gravatar for cpineau
4.4 years ago by
cpineau • 0
France
cpineau • 0 wrote:

Hi,

I try to groom a sequence from NCBI

sequenced from ilumina Hiseq 2000 by BGI,

it's running for more than 2 hours now. Is it normal ?

Is the tool doing an automatic detection of Fastq format ?

thanks for your help

Christophe

 

Tool name: FASTQ Groomer
Tool version: 1.0.4
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4
ToolShed URL: http://toolshed.g2.bx.psu.edu/view/devteam/fastq_groomer

 
fastq-groomer • 2.3k views
ADD COMMENT • link •
modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by cpineau • 0

Ok

it take more than 4 hours but my 9Gb of data are now "groomed"

regards 

Christophe

ADD REPLY • link written 4.4 years ago by cpineau • 0
0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If this is Illumina HIseq, then you probably can skip grooming next time and just assign the datatype ".fastqsanger".

Since the data is from an external source, I would recommend to always confirm datatype vs reported type, but you can check just the first 100 or so sequences per dataset (no need to process the whole thing). Use "Text manipulation -> Select first lines" and get the first 400 or so lines (some multiple of 4 for fastq), run FastQC, confirm type, then either directly assign datatype or groom. After assigning datatype, or grooming, is when you'll want to run FastQC on the entire dataset for QC purposes. More help here: http://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Sorry that the job seemed to take long to queue and run. The public Main Galaxy instance is busy. But maybe this will help speed things up with future data prep.

Jen, Galaxy team

 
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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