Need help with "FASTQ Summary Statistics" tool

Question: Need help with "FASTQ Summary Statistics" tool

4.5 years ago by

United States

damcpher • 0 wrote:

I imported some NGS files from EBI, but they came in the FASTQ.gz format. Is there a way to extract them or work with them in the workflow or is this going to require downloading, extracting, and then reuploading? P.S. That would be a total pain.

Tool name: FASTQ Summary Statistics
Tool version: 1.0.0
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0
ToolShed URL: http://toolshed.g2.bx.psu.edu/view/devteam/fastq_stats

fastq-summary-statistics • 2.4k views

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modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by damcpher • 0

4.5 years ago by

fubar ♦ 1.1k

Australia

fubar ♦ 1.1k wrote:

Try uploading your fastq.gz files - they should be transparently uncompressed - please see the same question answered here: tgz file uploading and supporting

Uploading as part of a workflow is not possible but all uploaded fastq.gz files in a history will be ordinary fastq datasets and should work fine as inputs in workflows AFAIK - please let us know if not.

Incidentally, the FastQC tool might worth trying - it generates very comprehensive summary statistics.

ADD COMMENT • link modified 4.5 years ago • written 4.5 years ago by fubar ♦ 1.1k

4.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

All of Ross's advice is right on target! I'm just going to add that depending on which file you upload (the original submitted versus the processed), you may need to groom the data. In either format, the datatype needs to modified to be ".fastqsanger" before proceeding with mapping, etc. (the default ".fastq" is not specific enough to define the quality score scaling, an important factor)

The wiki here explains how to check quality score type, modify with Fastq Groomer (if needed), and adjust datatype (the groomer tool does this when run on "submitted" that need it, but if you extract the "processed" it can usually just be assigned - but please double check the scaling yourself to confirm). The video uses example data from exactly this same source, so could be helpful in deciding how to build your workflow:
https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Take care, Jen, Galaxy team

ADD COMMENT • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

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