Using Bedtools to make a bed file for promoter

[Sanchari Sircar]

Hello,

I am trying to extract promoter locations based on the command:

bedtools flank -i A.txt -g SLy4_genome.size -l 2000 -r 0 -s

However, I am not getting any output. Sample files attached

Kindly help.

Thanks

cat A.txt

Chr0 93750 94430 Solyc00g500001 +

Chr0 305442 306257 Solyc00g500002 +

Chr0 311496 382066 Solyc00g500003 +

Chr0 417592 418482 Solyc00g500004 +

Chr0 478389 478640 Solyc00g500005 +

Chr0 481288 483182 Solyc00g500006 +

Chr0 497941 498614 Solyc00g500007 +

Chr0 531008 531682 Solyc00g500008 +

Chr0 531761 537711 Solyc00g500009 +

Chr0 544694 545489 Solyc00g500010 +

cat SLy4_genome.size

Chr0 9643250

Chr1 90863682

Chr2 53473368

Chr3 65298490

Chr4 64459972

Chr5 65269487

Chr6 47258699

Chr7 67883646

Chr8 63995357

Chr9 68513564

Chr10 64792705

Chr11 54379777

Chr12 66688036

[Aaron Quinlan]

This is because your strand indicator is in the 5th instead of the expected 6th column, as defined by the BED specification. It works if you remove the “-s” argument and will work if you add a mock 5th column before the strand.

Aaron

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