started igv range tool

chipseq_workflow/igv_track_range.sh

+docopts...
+
+opts$bamfile
+...
+
+
+bamFile=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/data/alignments_mmfilt/K4M_Oblong_mmf.bam
+bamBaseName=$(basename $bamFile .bam)
+genomeCoverageBed -d -ibam $bamFile | head -n1000000 | cut -f3 | sort | uniq -c | trim > ${bamBaseName}.coveragedist.txt
+
+echo '
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
+require(ggplot2)
+
+covDist = read.delim("K4M_Oblong_mmf.coveragedist.txt", header=F, sep=" ") %>% rename(num_bases=V1, coverage=V2)
+
+covDist %<>% arrange(coverage) %>% mutate(total_cov=sum(coverage), cum_coverage=cumsum(coverage), cum_cov_prop=cum_coverage/total_cov)
+
+covDist %>% ggplot(aes(coverage, cum_cov_prop)) + geom_area()
+' | R --vanilla
\ No newline at end of file