Bedtools to make a bed file for promoter

Question

[pixie@bioinfo]

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 given below 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

Answer 1

[seidel]

You're not getting any output because your BED file is not the correct format. You have strand in the 5th column, but BED format has strand in the 6th column.

1   chrom
2   chromStart
3   chromEndchromStart.
4   name
5   score   Score between 0 and 1000
6   strand

You can substitute a period for the score.

Chr0    93750   94430   Solyc00g500001 . +
Chr0    305442  306257  Solyc00g500002 . +
Chr0    311496  382066  Solyc00g500003 . +