cbirdlab / dDocentHPC

hard fork of dDocent, edited to run without interactive user input
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CNV map instructions in config file #1

Open jdselwyn opened 5 years ago

jdselwyn commented 5 years ago

Need to update instructions because first column of pop.map file returns entire column name and the cnv file doesn't need the cutoffs.

popmap file: FCOP-1_GAGTGG_L004.1.1-RG.bam FCOP-1 FCOP-2_GATCAG_L004.1.1-RG.bam FCOP-2 FMAT-1_GTTTCG_L004.1.1-RG.bam FMAT-1 FMAT-2_GTGGCC_L004.1.1-RG.bam FMAT-2 FSAN-1_TAGCTT_L004.1.1-RG.bam FSAN-1 FSAN-2_GGCTAC_L004.1.1-RG.bam FSAN-2

CNV file: FCOP-1_GAGTGG_L004 10 FCOP-2_GATCAG_L004 10 FMAT-1_GTTTCG_L004 10 FMAT-2_GTGGCC_L004 9 FSAN-1_TAGCTT_L004 10 FSAN-2_GGCTAC_L004 9

cbird808 commented 4 years ago

I updated the config.4.all, leaving this open for now until I figure out exactly why this difference is necessary.