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Question: Need help with "FastQC:Read QC" tool
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gravatar for jianwang
3.8 years ago by
jianwang • 0
United States
jianwang • 0 wrote:

I have collected the raw data for my RNA-seq project. This dataset includes short DNA sequences of 12 samples, but each sample has multiply files (11-15). How and in which step can I combine the data for each sample together? Many thanks.

Jian

 

Tool name: FastQC:Read QC
Tool version: 0.52
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.52
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/fastqc

 
rna-seq tophat fastqc:read-qc cufflinks • 1.5k views
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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by jianwang • 0
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gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

To merge together multiple fastq files from distinct runs belonging to the same exact sample - use the tool Text Manipulation: Concatenate datasets. This tool will actual merge together many datatypes - in any way you want - keeping the logic of the data grouping is for you to organize (and label).

Then run the FastQC tool on each sample. Or you can run it on each run independently - may provide more useful stats if the data are from different runs, as some may have had problems and others not. Then merge by sample after. You definitely want to keep sample datasets together, distinct from each other, when going forward from here, including fwd and rev reads in distinct datasets, through QC and mapping. For example, at the end once merged and quality scores adjusted (as needed), run FastQC as a final QA step to gather metrics on the final inputs. If you do more QC, run again. Then proceed to mapping.

This changes after mapping and read groups have been added to the SAM/BAM datasets. For RNA-Seq analysis, keep these distinct by sample throughout. But for variant analysis, you often want to merge these before performing the calls. See the Picard tool group to merge BAM datasets.

See our Support wiki for help with Fastq formatting and other common analysis Qs:
https://wiki.galaxyproject.org/Support
 

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
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