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jwschroeder3jwschroeder3
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‎README.md‎

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@@ -44,7 +44,9 @@ a `fix` argument that could be helpful.
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Enter directory containing sample info file
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(see `examples/nonstranded_sample_info.txt` and
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`examples/stranded_sample_info.txt` for sample info file templates).
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`examples/stranded_sample_info.txt` for sample info file templates.
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Note: the norm_factor column of these files is currently ignored, but
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just has to be present.).
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Run the following,
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substituting the location of the `enricherator` source tree for
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`<srcdir>`. You will also need to adjust several of the arguments

‎examples/nonstranded_sample_info.txt‎

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genotype,sample,rep,strand,file
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py79,input,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep1_input_both_strand_counts_with_strand_col.bedgraph
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py79,input,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep2_input_both_strand_counts_with_strand_col.bedgraph
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py79,hbd,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep1_hbd_both_strand_counts_with_strand_col.bedgraph
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py79,hbd,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep2_hbd_both_strand_counts_with_strand_col.bedgraph
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rnhB,input,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep1_input_both_strand_counts_with_strand_col.bedgraph
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rnhB,input,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep2_input_both_strand_counts_with_strand_col.bedgraph
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rnhB,hbd,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep1_hbd_both_strand_counts_with_strand_col.bedgraph
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rnhB,hbd,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep2_hbd_both_strand_counts_with_strand_col.bedgraph
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rnhC,input,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep1_input_both_strand_counts_with_strand_col.bedgraph
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rnhC,input,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep2_input_both_strand_counts_with_strand_col.bedgraph
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rnhC,hbd,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep1_hbd_both_strand_counts_with_strand_col.bedgraph
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rnhC,hbd,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep2_hbd_both_strand_counts_with_strand_col.bedgraph
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genotype,sample,rep,strand,file,norm_factor
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py79,input,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep1_input_both_strand_counts_with_strand_col.bedgraph,1
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py79,input,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep2_input_both_strand_counts_with_strand_col.bedgraph,1
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py79,hbd,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep1_hbd_both_strand_counts_with_strand_col.bedgraph,1
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py79,hbd,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep2_hbd_both_strand_counts_with_strand_col.bedgraph,1
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rnhB,input,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep1_input_both_strand_counts_with_strand_col.bedgraph,1
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rnhB,input,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep2_input_both_strand_counts_with_strand_col.bedgraph,1
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rnhB,hbd,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep1_hbd_both_strand_counts_with_strand_col.bedgraph,1
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rnhB,hbd,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep2_hbd_both_strand_counts_with_strand_col.bedgraph,1
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rnhC,input,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep1_input_both_strand_counts_with_strand_col.bedgraph,1
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rnhC,input,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep2_input_both_strand_counts_with_strand_col.bedgraph,1
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rnhC,hbd,rep1,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep1_hbd_both_strand_counts_with_strand_col.bedgraph,1
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rnhC,hbd,rep2,both,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep2_hbd_both_strand_counts_with_strand_col.bedgraph,1

‎examples/stranded_sample_info.txt‎

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genotype,sample,rep,strand,file
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py79,input,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep1_input_plus_strand_counts_with_strand_col.bedgraph
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py79,input,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep1_input_minus_strand_counts_with_strand_col.bedgraph
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py79,input,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep2_input_plus_strand_counts_with_strand_col.bedgraph
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py79,input,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep2_input_minus_strand_counts_with_strand_col.bedgraph
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py79,hbd,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep1_hbd_plus_strand_counts_with_strand_col.bedgraph
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py79,hbd,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep1_hbd_minus_strand_counts_with_strand_col.bedgraph
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py79,hbd,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep2_hbd_plus_strand_counts_with_strand_col.bedgraph
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py79,hbd,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep2_hbd_minus_strand_counts_with_strand_col.bedgraph
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rnhB,input,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep1_input_plus_strand_counts_with_strand_col.bedgraph
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rnhB,input,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep1_input_minus_strand_counts_with_strand_col.bedgraph
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rnhB,input,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep2_input_plus_strand_counts_with_strand_col.bedgraph
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rnhB,input,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep2_input_minus_strand_counts_with_strand_col.bedgraph
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rnhB,hbd,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep1_hbd_plus_strand_counts_with_strand_col.bedgraph
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rnhB,hbd,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep1_hbd_minus_strand_counts_with_strand_col.bedgraph
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rnhB,hbd,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep2_hbd_plus_strand_counts_with_strand_col.bedgraph
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rnhB,hbd,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep2_hbd_minus_strand_counts_with_strand_col.bedgraph
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rnhC,input,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep1_input_plus_strand_counts_with_strand_col.bedgraph
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rnhC,input,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep1_input_minus_strand_counts_with_strand_col.bedgraph
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rnhC,input,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep2_input_plus_strand_counts_with_strand_col.bedgraph
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rnhC,input,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep2_input_minus_strand_counts_with_strand_col.bedgraph
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rnhC,hbd,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep1_hbd_plus_strand_counts_with_strand_col.bedgraph
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rnhC,hbd,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep1_hbd_minus_strand_counts_with_strand_col.bedgraph
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rnhC,hbd,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep2_hbd_plus_strand_counts_with_strand_col.bedgraph
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rnhC,hbd,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep2_hbd_minus_strand_counts_with_strand_col.bedgraph
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genotype,sample,rep,strand,file,norm_factor
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py79,input,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep1_input_plus_strand_counts_with_strand_col.bedgraph,1
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py79,input,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep1_input_minus_strand_counts_with_strand_col.bedgraph,1
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py79,input,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep2_input_plus_strand_counts_with_strand_col.bedgraph,1
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py79,input,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/input/bootstrap/py79_rep2_input_minus_strand_counts_with_strand_col.bedgraph,1
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py79,hbd,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep1_hbd_plus_strand_counts_with_strand_col.bedgraph,1
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py79,hbd,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep1_hbd_minus_strand_counts_with_strand_col.bedgraph,1
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py79,hbd,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep2_hbd_plus_strand_counts_with_strand_col.bedgraph,1
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py79,hbd,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/py79/hbd/bootstrap/py79_rep2_hbd_minus_strand_counts_with_strand_col.bedgraph,1
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rnhB,input,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep1_input_plus_strand_counts_with_strand_col.bedgraph,1
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rnhB,input,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep1_input_minus_strand_counts_with_strand_col.bedgraph,1
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rnhB,input,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep2_input_plus_strand_counts_with_strand_col.bedgraph,1
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rnhB,input,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/input/bootstrap/rnhB_rep2_input_minus_strand_counts_with_strand_col.bedgraph,1
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rnhB,hbd,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep1_hbd_plus_strand_counts_with_strand_col.bedgraph,1
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rnhB,hbd,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep1_hbd_minus_strand_counts_with_strand_col.bedgraph,1
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rnhB,hbd,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep2_hbd_plus_strand_counts_with_strand_col.bedgraph,1
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rnhB,hbd,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhB/hbd/bootstrap/rnhB_rep2_hbd_minus_strand_counts_with_strand_col.bedgraph,1
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rnhC,input,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep1_input_plus_strand_counts_with_strand_col.bedgraph,1
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rnhC,input,rep1,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep1_input_minus_strand_counts_with_strand_col.bedgraph,1
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rnhC,input,rep2,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep2_input_plus_strand_counts_with_strand_col.bedgraph,1
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rnhC,input,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/input/bootstrap/rnhC_rep2_input_minus_strand_counts_with_strand_col.bedgraph,1
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rnhC,hbd,rep1,plus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep1_hbd_plus_strand_counts_with_strand_col.bedgraph,1
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rnhC,hbd,rep2,minus,/corexfs/schroedj/stranded_hbd_enrichment/rnhC/hbd/bootstrap/rnhC_rep2_hbd_minus_strand_counts_with_strand_col.bedgraph,1

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