after hicup, rmap baitmap and runchicago.r

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Issue #39 new
Dimitris Hat created an issue

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]?

Comments (7)

  1. 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.

  2. 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.

  3. Dimitris Hat reporter

    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/

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