diff --git a/dunnart/Snakefile b/dunnart/Snakefile index 0ae59b3a962cfede76ef8e3be3653d35e95cad72..1abbeb800d4d50bc98b4084eef10c95ee3cbbbff 100644 --- a/dunnart/Snakefile +++ b/dunnart/Snakefile @@ -460,11 +460,14 @@ rule subsample_aligned_reads: shell("zcat {input} > {output.tmp}") # Determine exclusion range for fragment length estimation. +## From bamPEFragmentSize (deepTools) average fragment length is ~220bp +## See bamPEFragmentSize.histogram.png # Use a fixed lowerbound at -500. -# Upperbound EXCLUSION_RANGE_MAX is +# Upperbound E +#EXCLUSION_RANGE_MAX is # Histone ChIP-seq: max(read_len + 10, 100) # lowerbound is fixed at 500 for both -# read length is 50 because that is what we trimmed it to?? + rule cross_correlation_SSP: input: