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TCP-Lab / x.FASTQ

Bash wrapper modules for the remote analysis of RNA-Seq data, with persistency features.
MIT License
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Add the --raw option to `countfastq.sh` #11

Closed MrHedmad closed 8 months ago

MrHedmad commented 9 months ago

This fixes #9.

The --raw flag makes countfastq to not include the name of the metric in the output columns. For example:

countfastq --metric="expected_count" -r
head Count_Matrix_genes_expected_count.tsv

results in

gene_id SRR222175   SRR222176   SRR222177   SRR222178
ENSG00000000003 282 161 709 666.68
ENSG00000000005 3   0   0   3
ENSG00000000419 59  84.71   149 349.92
ENSG00000000457 47.06   39.7    145.78  172.9
ENSG00000000460 4.95    8.3 31.22   84.11
ENSG00000000938 34  73  64  44
ENSG00000000971 84.61   100.92  695.31  476.76
ENSG00000001036 188.71  291 561.01  596.2
ENSG00000001084 76.83   80.83   268.85  342.88