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Old 05-04-2018, 11:06 AM   #1
cursecatcher
Junior Member
 
Location: Italy

Join Date: May 2018
Posts: 5
Unhappy Unable to intersect BAM file with bedtools

Hi everyone, I'm trying to use bedtools intersect to check the number of mapped reads in target regions (in a .bed file) originated by targeted bisulfite sequencing experiment (EpiSeq Roche).

I used the following command.

Code:
./bedtools intersect -bed -abam sample2.bam -b 
 ~/Data/MethylSeq/dataset/Agesmoke_dataset/AgeSmkSop_all_primary_targets.bed
The program terminate with the following message and no result at all.

Code:
* WARNING: File sample2.bam has inconsistent naming convention for record:
NC_000016.9  24163386  24163537  M03971:33:000000000-BN5NL:1:2114:12003:16132/1  255  +

* WARNING: File sample2.bam has inconsistent naming convention for record:
NC_000016.9  24163386  24163537  M03971:33:000000000-BN5NL:1:2114:12003:16132/1  255  +
I tried to modify the original SAM file removing the read that cause the problem (that was the first read in the SAM file) and the problem persists with the second read. I tried also the option -nonamecheck with no results.

Can someone help us? Thank you.
Nicola
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