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different between feature_counts.dir/genesetexons.feature_counts.tsv.gz and gene_counts.dir/genesetexons.gene_counts.tsv.gz #141

Closed csandorfr closed 7 years ago

csandorfr commented 9 years ago

Hi,

These two read count file are make when I run pipeline_rnaseqdiffexpression.py loadDESeq

I was wondering what is the different between two file. I know that it is the first that is considered in DESeq analyses.

Thanks

Cynthia

jethrojohnson commented 9 years ago

Hi Cynthia,

The difference is in the tool used to create the count tables passed to DESeq.

The first file uses feature counts to create the count table, where as the second uses the CGAT script gtf2table. Any differences between these two files should be due to the parameters passed to featureCounts, which can be specified in the pipeline.ini file.

If you are interested in how gtf2table is run, then have a look at the ruffus task buildGeneLevelRead counts in pipeline_rnaseqdiffexpression.py

Thanks

Jethro

On 02/18/15 10:36, csandorfr wrote:

Hi,

These two read count file are make when I run pipeline_rnaseqdiffexpression.py loadDESeq

I was wondering what is the different between two file. I know that it is the first that is considered in DESeq analyses.

Thanks

Cynthia

— Reply to this email directly or view it on GitHub https://github.com/CGATOxford/cgat/issues/141.

Dr Jethro Johnson CGAT Genomics Training Fellow MRC Functional Genomics Unit University of Oxford +44 1865 282362