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sjroth / ARTDeco

MIT License
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Metafile not properly formatted #5

Closed pillailab closed 3 years ago

pillailab commented 3 years ago

I am running the process mode and my bam file list looks like below: MPR85_STAR_Aligned.sortedByCoord.out.bam
MPR86_STAR_Aligned.sortedByCoord.out.bam
MPR90_STAR_Aligned.sortedByCoord.out.bam MPR91_STAR_Aligned.sortedByCoord.out.bam

I formatted the metafile.txt as below: Experiment Group MPR85_R1 WT_Total MPR86_R2 WT_Total MPR90_R1 Mut_Total MPR91_R2 Mut_Total When i run the preprocess command as below: ARTDeco -mode preprocess -gtf-file modified_gencode.v22.annotation.gtf.gtf -chrom-sizes-file GRCh38.genome.chrom.sizes -home-dir ~/scratch60/SF3B1_PRC2/March_2021/ARTDeco -bam-files-dir ~/scratch60/SF3B1_PRC2/March_2021/ARTDeco/bam/ -cpu 1 -meta-file ~/scratch60/SF3B1_PRC2/March_2021/ARTDeco/meta.txt I get the following error: Running preprocess mode... Loading ARTDeco file structure... Meta file not properly formatted... Exiting...

The format for metafile is not very clear - what am i doing wrong ? thanks Manoj

sjroth commented 3 years ago

Hi Manoj,

Your labels are not consistent with your bam file names. ARTDeco takes the prefix (everything before the .bam extension) as the name for the experiment. You need to either rename your files or rename the experiments.

Best, Sam

pillailab commented 3 years ago

wow - fast response ! that worked - thanks a lot. Manoj