script to run CrossMap for a set of bam files
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9.6 years ago

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"))}
genome Assembly R • 3.0k views
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why using R ?

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

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@Pierre, what would be the best option?

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@Pierre i could not get you

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a simple bash script...

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Do you mind providing a example?

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