Question: bedtools multicov displays only the last BED feature
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gravatar for ThePresident
2.5 years ago by
ThePresident140
ThePresident140 wrote:

I want to count the number of reads that fall in some predefined regions of a genome. Normally, this can be easily done with bedtools multicov. I have sorted and indexed bam files of my alignments. I created a BED file with my regions of interest (excel, then saved as tab-delimited, and added .bed extension).

Here's what BED file look like:

Chr1    500000  505001  
Chr1    1000000 1001001 
Chr1    2000000 2000251 
Chr1    2500000 2500101

I run bedtools with this command:

bedtools multicov -bams ./*.bam -bed bedfile.bed

I have 5 bam files in the same directory, as well as 5 corresponding .bai index files. I get read counts for all 5 bam files but only for the last feature of the bed file, whatever the last line is. If I add more features it will still give me the counts for the last one only. Any idea what's wrong?

Thanks, TP

multicov bedtools • 1.2k views
ADD COMMENTlink modified 8 months ago by rania.hamdy10 • written 2.5 years ago by ThePresident140

I made another BED file in a text editor and this time it worked. I have no idea what was wrong with my BED file...

ADD REPLYlink written 2.5 years ago by ThePresident140

Was it made on Windows?

ADD REPLYlink written 2.5 years ago by WouterDeCoster42k

It was made on mac OS

ADD REPLYlink written 2.5 years ago by ThePresident140

I want to count histone modification reads that fall in some predefined regions of a genome using bedtools multicov command i cant understand what BED file refer to How can I know my regions of interest?? on what basis i will create it ? can you help me please?

ADD REPLYlink written 8 months ago by rania.hamdy10
0
gravatar for rania.hamdy1
8 months ago by
rania.hamdy10 wrote:

I want to count histone modification reads that fall in some predefined regions of a genome using bedtools multicov command i cant understand what BED file refer to How can I know my regions of interest?? on what basis i will create it ? can you help me please?

ADD COMMENTlink modified 8 months ago • written 8 months ago by rania.hamdy10
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