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GiantSpaceRobot / tsRNAsearch

Nextflow DSL2 tRNA and ncRNA fragment identification pipeline for small RNA-seq data
MIT License
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Sorting Issue #8

Closed mouzkolit closed 2 years ago

mouzkolit commented 2 years ago

Hey,

I recently noticed a Bug in the software. Whenever you specify your file for the group comparsion (layout file). It seems that the sample names are automatically sorted so that the group annotation for each file is not considered and therefore the group name not assigned accordingly.

As an example if I've samples called

1901_0001.fq.gz, ctrl 1905_0001.fq.gz, ctrl 1902_0001.fq.gz, ko 1903_0001.fq.gz, ko

the 1902 and the 1901 sample are considered as ctrl sample and the 03,05 sample as ko sample for the group analysis while the layout annotation file is neglected. Hope this helps to improve the situation.

Otherwise nice tool!

GiantSpaceRobot commented 2 years ago

Thanks for letting me know, and apologies for the delay. The problem was within the DESeq2 script I had written, where the filenames were getting listed alphanumerically instead of in the provided order from the layout file. This is now fixed. Paul