after hicup, rmap baitmap and runchicago.r

[Dimitris Hat]

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]?

[Mikhail Spivakov]

It might help for you to check out the .rmap and .baitmap files from our published datasets. Please see here: https://osf.io/dnzpe/

The command line: ./bam2chicago.sh myfile.bam my.baitmap my.rmap samplename is correct, [nodelete] is an optional parameter that I suggest you don't use.

[Dimitris Hat]

ok, i got them. But at the sample name i need a .bedpe file?

[Mikhail Spivakov]

Samplename is just the name of the folder, in which you want to store your results. Please refer to the README file for chicagoTools for more details.

[Dimitris Hat]

i did just put an output folder that i named test1 , and this is the output :

Can't open test1//test_dataset1_2.hicup_mappedToBaitsBoRAndRFrag_fmore06.bedpe: No such file or directory. rm: cannot remove 'test1//test_dataset1_2.hicup_mappedToBaitsBoRAndRFrag_fmore06.bedpe': No such file or directory

my command is : ./bam2chicago.sh '/home/app/Desktop/apps/HiCUP-master/output/test_dataset1_2.hicup.bam' '/home/app/Desktop/apps/chicagoTeam/test/Human_hg19/Digest_Human_HindIII_baits_e75_ID.baitmap' '/home/app/Desktop/apps/chicagoTeam/test/Human_hg19/Digest_Human_HindIII.rmap' test1/

[Dimitris Hat]