This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
BSD 3-Clause "New" or "Revised" License
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Adding flags to simulate SET from PET bams in lines 448-450 (run_spp.R) #1
I am looking at lines 448-450 in run_spp.R and it looks like one can simulate RSC and NSC computation on PET bam file, by running adding samtools flags to select only the first mate or second mate in lines 448-450. Ideally one could compute both ways and report the average? Is there something I missed?
It would save some compute if one doesn't have to write bam files containing only one mate when run_spp.R does the tagaAlign conversion anyway.
I am looking at lines 448-450 in run_spp.R and it looks like one can simulate RSC and NSC computation on PET bam file, by running adding samtools flags to select only the first mate or second mate in lines 448-450. Ideally one could compute both ways and report the average? Is there something I missed?
It would save some compute if one doesn't have to write bam files containing only one mate when run_spp.R does the tagaAlign conversion anyway.