bedtools multicov - tab-delimited bam files?

Question

[susibing]

Dear all,

I am trying to use bedtools multicov using six bam files as input and a gff file to compare with and unfortunately receive the error message: "It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited?"

Does anyone know how to find out whether a bam file is delimited or not? And how to change that?

This is the first 5 lines of one of the bam files:

SRR2960489.11401.1      0       chr1    629572  255     31M     *       0       0       AGTAAGGTCAGCTAATTAAGCTATCGGGCCC BBBFFFFFFFFFFIIIIIIIIIIIIIIIIII XA:i:0  MD:Z:15A15      NM:i:1
SRR2960489.33430.1      0       chr1    629572  255     31M     *       0       0       AGTAAGGTCAGCTAATTAAGCTATCGGGCCC BBBFFFFFFFFFFIIIIIIIIIIIIIIIIII XA:i:0  MD:Z:15A15      NM:i:1
SRR2960489.48476.1      0       chr1    629572  255     31M     *       0       0       AGTAAGGTCAGCTAATTAAGCTATCGGGCCC BBBFFFFFFFFFFFIIIIFFFFFFFFFFFFI XA:i:0  MD:Z:15A15      NM:i:1
SRR2960489.50759.1      0       chr1    629572  255     31M     *       0       0       AGTAAGGTCAGCTAATTAAGCTATCGGGCCA BBBFFFFFFFFFFIIIIIIIIIIIIIIIIII XA:i:0  MD:Z:15A14C0    NM:i:2
SRR2960489.71848.1      0       chr1    629572  255     31M     *       0       0       AGTAAGGTCAGCTAATTAAGCTATCGGGCCC BBBFFFFFFFFFFIIIIIIIIIIIIIIIIII XA:i:0  MD:Z:15A15      NM:i:1

I am new to both samtools and bedtools and happy to hear about any suggestions from you.

Thanks in advance

[Ankit]

What is the command of your bedtools multicov? Did you sort your bam and indexed?

[Vitis]

Looks like the error message is not referring to the BAM files but the input BED file specifying the interval/loci for coverage calculation. Can you post the first few lines of the input BED file?

Answer 1

[susibing]

Thanks! It was indeed the gff input file that was not tab-delimited.. Thank you very much. (Feeling kind of stupid now..)