Hello again. Finally hicup worked so now i got the bam file. In order to run the bam2chicago.sh <bamfile> <baitmap-file> <digest-rmap-file> <sample-name> [nodelete].
My question is :
In oder to have the baitmap and rmap i have to run create_baitmap_rmap.pl which needs i) digest file ii)oligos file , i have the digest file from hicup - i dont have the oligos file - where do i get that? Also i found out here that you can create the baitmap and rmap yourself from the digest file. "Make the .rmap file by taking the first 3 columns of the HiCUP digest file and assigning an arbitrary "numeric ID" " so 4th column is just a number 1...to whatever and saving it as .rmap.csv ? then deleting the .csv? Also " All you need to do to make a baitmap file is take the subset of .rmap rows that corresponds to baited fragments and save them as .baitmap. " i have no idea what that means. Isnt there a simpler way?
and finally when i got all these files the command is : ./bam2chicago.sh myfile.bam my.baitmap my.rmap samplename? [nodelete]?