Using Bedtools to make a bed file for promoter

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Sanchari Sircar

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Oct 11, 2020, 7:57:38 PM10/11/20
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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

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Oct 12, 2020, 9:33:58 AM10/12/20
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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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