bam2chicago bedtools error

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Issue #14 resolved
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Im getting an error when I run the script and Im not sure why. This is my error message but when I check the number of columns in the output file all the rows have 14 columns

Checking rmap and baitmap files... Rmap and baitmap files checked successfully Processing sample Chic_S2... Using bam file Chic_S2_R1_2.hicup.bam Using baitmap file /scratch/rr1859/PR_Chic/chicago/all_dpn_frags_Mer41_CS_forDpn_baits_rmap.baitmap Using digest map (rmap) file /scratch/rr1859/PR_Chic/chicago/hg19_dpn.rmap Baitmap file contains >4 columns. Checking if /scratch/rr1859/PR_Chic/chicago/all_dpn_frags_Mer41_CS_forDpn_baits_rmap.baitmap_4col.txt exists... Found /scratch/rr1859/PR_Chic/chicago/all_dpn_frags_Mer41_CS_forDpn_baits_rmap.baitmap_4col.txt Intersecting with bait fragments (using min overhang of 0.6)... Flipping all reads that overlap with the bait on to the right-hand side... Intersecting with bait fragments again to produce a list of bait-to-bait interactions that can be used separately; note they will also be retained in the main output... Error: line number 14 of file Chic_S2/Chic_S2_R1_2.hicup_mappedToBaits_baitOnRight.bedpe has 15 fields, but 14 were expected.

Comments (3)

  1. Mikhail Spivakov

    This error is generated by bedtools, and in our experience usually results from whitespace characters in the input file.

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