Question: script to run CrossMap for a set of bam files
0
gravatar for ifudontmind_plzz
4.5 years ago by
Netherlands
ifudontmind_plzz130 wrote:

I was trying to run CrossMap for a set of bam files using this script. But its showing error.

bam_list <- list.files(path = “home_hg19_Bam/", pattern = ".bam$", full.names=T)

for (i in 1:length(bam_list)){
system(paste0(“CrossMap.py bam ./hg18ToHg19.over.chain.gz”,  bam_list[i], folder, “home/SCLC_hg19_Bam/“ ,gsub(".bam", "", bam_list[i]), “_hg19.bam”))}

 

assembly R genome • 1.5k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 4.5 years ago by ifudontmind_plzz130

why using R ?

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum122k

set the full patch to CrossMap.py, add the python interpreter :" /usr/bin/python /path/to/CrossMap.py ...."

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum122k

@ Pierre Lindenbaum, what  would be the best option ?

ADD REPLYlink written 4.5 years ago by ifudontmind_plzz130

@Pierre i could not get you

ADD REPLYlink written 4.5 years ago by ifudontmind_plzz130

a simple bash script...

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum122k

do you mind providing a example. 

ADD REPLYlink written 4.5 years ago by ifudontmind_plzz130

http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-7.html

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum122k
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