Question: script to run CrossMap for a set of bam files
0
gravatar for ifudontmind_plzz
4.0 years ago by
Netherlands
ifudontmind_plzz110 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 • 1.3k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.0 years ago by ifudontmind_plzz110

why using R ?

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum118k

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

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum118k

@ Pierre Lindenbaum, what  would be the best option ?

ADD REPLYlink written 4.0 years ago by ifudontmind_plzz110

@Pierre i could not get you

ADD REPLYlink written 4.0 years ago by ifudontmind_plzz110

a simple bash script...

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum118k

do you mind providing a example. 

ADD REPLYlink written 4.0 years ago by ifudontmind_plzz110

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

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum118k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1803 users visited in the last hour