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Old 11-05-2013, 12:04 AM   #9
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311

Originally Posted by jazz View Post
Here is the command I tried:

intersectbed -a Inputfile.bed -b compare.gff > output.bed

The first few lines of the resulting bed file look like this:

BAM◊%@HD VN:1.0 SO:unsorted
@SQ SN:scaffold16 LN:1343
@SQ SN:scaffold6 LN:1021
@SQ SN:scaffold4 LN:958
@SQ SN:scaffold22 LN:923
Hi- I suspect your "Inputfile.bed" is not a bed file as the name suggests but a bam file. Could you post the output of:

head Inputfile.bed 
head compare.gff
If Inputfile.bed is indeed a bam file you should use something like (depending on exactly what output you want):
intersectBed -abam Inputfile.bam -b compare.gff -bed -wb > results.bed
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