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Commit bbeb4524 authored by Venkat Malladi's avatar Venkat Malladi
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Changed to bedSort.

parent 45277ef8
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workflow/scripts/call_peaks_macs.py
+ 2
− 4
View file @ bbeb4524
...@@ -175,8 +175,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes) ...@@ -175,8 +175,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Sort file # Sort file
out, err = utils.run_pipe([ out, err = utils.run_pipe([
'sort -k1,1 -k2,2n %s' % (fc_bedgraph_fn)], 'bedSort %s %s' % (fc_bedgraph_fn, fc_bedgraph_sorted_fn)])
fc_bedgraph_sorted_fn)
# Convert bedgraph to bigwig # Convert bedgraph to bigwig
command = 'bedGraphToBigWig ' + \ command = 'bedGraphToBigWig ' + \
...@@ -223,8 +222,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes) ...@@ -223,8 +222,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Sort file # Sort file
out, err = utils.run_pipe([ out, err = utils.run_pipe([
'sort -k1,1 -k2,2n %s' % (fc_bedgraph_fn)], 'bedSort %s %s' % (fc_bedgraph_fn, pvalue_bedgraph_sorted_fn)])
pvalue_bedgraph_sorted_fn)
# Convert bedgraph to bigwig # Convert bedgraph to bigwig
command = 'bedGraphToBigWig ' + \ command = 'bedGraphToBigWig ' + \
......
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