Bedtools intersect error: ***** ERROR: Unrecognized parameter: –b *****

[mhc...@gmail.com]

I am trying to intersect a list of variants with a bed file of genomic regions. My command, and the error message, are as follows:

$ bedtools intersect -a HSAN5-c_WG.step7.varlist –b Khurana_US_regions.bed -wa -wb > HSAN5-c__FANTOM5_US_variants

***** ERROR: Unrecognized parameter: –b *****
***** ERROR: Unrecognized parameter: test.bed *****

My .bed file looks like this (it was a .txt file that I renamed to a .bed file):

$ head Khurana_US_regions.bed
chr1    714066  714076  FOS.motif       Sensitive
chr1    714066  714076  JUN.motif       Sensitive
chr1    714091  714101  FOS.motif       Sensitive
chr1    714091  714101  JUN.motif       Sensitive
chr1    714123  714133  FOS.motif       Sensitive
chr1    714123  714133  JUN.motif       Sensitive
chr1    752140  752290  DHS.Spinal.cord Sensitive
chr1    767611  767623  FOXA1.motif     Sensitive
chr1    778431  778442  GATA2.motif     Sensitive
chr1    822797  823589  BDP1.peak       Sensitive

I'm not sure what the issue is here with the bed file. I thought Bedtools only looked at the first 3 columns of the file. Can anyone help me?

Thanks,
Madeline

[Aaron Quinlan]

Hi Madeline,

The error is odd in that your command makes no use of a file called test.bed. However, it looks the the "dash" in "-b" is Unicode not ASCII and is different than the seemingly correct dash in "-a". I think this is the cause of your problem. Could you try retyping the dask in "-b"?

Aaron

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[mhc...@gmail.com]

Yes, it seems the problem was just the dash in front of the b. Thank you!

[mhc...@gmail.com]

Ah sorry the error is :***** ERROR: Unrecognized parameter: –b *****
***** ERROR: Unrecognized parameter: Khurana_US_regions.bed *****

On Thursday, October 22, 2015 at 11:52:22 AM UTC-7, mhc...@gmail.com wrote: