Hello! :)

I would like to compute the coverage for my file.bam using the information of the file.bed.

My file bed is like this:

chr1    12594   12721   uc010nxq.1_cds_1_0_chr1_12595_f 0   +
chr1    13402   13639   uc010nxq.1_cds_2_0_chr1_13403_f 0   +
chr1    69090   70008   uc001aal.1_cds_0_0_chr1_69091_f 0   +

And I would like to have something like that:

chr1      12594    12721    40
chr1      13402    13639    68

where the IV column is the coverage.

The read in my bam file (I have converted it to sam format in order to check if the chromosome ids in the bam file do not exactly match in the bed file) are like that:

H-D00:95:C62BPANXX:1:2315:2019:91137    163 chr1    10002   38  4S77M1I43M  =   10114   237 CCCAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTACCCCTAACCCAAACCTAACCCTA   A@?BCEGFFGDFGFFGDFGFFGDFGFEGDFGFFGDEGFFG@FGFFFDEGEFF@F/BAG/5/EB4;@GE?G/1.BCGAEBFFC3@@GBBDDFGC04<FGF##########################   MC:Z:125M   BD:Z:MMKNOGPPLMNNNOKLMMNOKLMLMNJKLLMNJKLLMNJKLLMNJKLLMNJKLLMNJKLLMOKKLLMOKLMMNOKLMLMOJLLLMMNJLMMNOKLMMNOMMMMMMMMMMMMMNNNNNNOOPMMMM  MD:Z:97A11C10   -PG:Z:MarkDuplicates    RG:Z:HTG-1  BI:Z:QQMTRKRRMSSOQPLRROPPLRROPPKRQOPPLRROPPLRROPPLRROPPLRROPPLSRPPQMSSPQQMSSPQQMSSPQQMSQQPQQMSSPQQMSTQRRRRRRRRRRRRRSSRSSSSSSTUQQQQ  NM:i:3  MQ:i:38 AS:i:103    XS:i:97

I have read this post Tools To Calculate Average Coverage For A Bam File? and first I have tried to compute it with

genomeCoverageBed

but it gave the results for each base.

After that I have tried the following tool and command:

bedtools coverage -a file.bed -b alignment.bam > output

but nothing happened, the output file was empty.

Do you have any suggestions?

Thank you in advance