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converting txt to bed

I have this txt file by pasting different columns now how I can convert that to bed please because I need a bed then sorting that

I used

[izadi@lbox161 merged_asmribo]$ cut -f 1,2,3,4,5,6 main.txt > main.bed
cut: fields and positions are numbered from 1
Try 'cut --help' for more information.

 FLP1    252    1523
  RAF1    3271    3816
  REP1    1887    3008
  REP2    5308    6198
  YAL069W    335    649
  YAL068W-A    538    792
  YAL067W-A    2480    2707
  YAL066W    10092    10400
  YAL064W-B    12047    12427
  YAL064W    21526    21852
rna-seq
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updated by Ram Ram • written by zizigolu zizigolu

What you pasted looks like BED file already.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Devon Ryan is right, your file already looks like a bed file. Are you expecting something different? Perhaps something like:

chr1    252    1523    FLP1
chr2    3271    3816    RAF1
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updated by Ram Ram • written by h.mon h.mon

1 answer

This requires rather a simple text manipulation trick. The key is that you need to know exactly what you want as a BED file. Read more about BED format here.

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updated by Ram Ram • written by biocyberman biocyberman

thank you all, I need gene name, start, end, mapping quality

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updated by Ram Ram • written by zizigolu zizigolu

You'll need to show what you have to start with. If it's what you posted then you can't add the mapping quality, because you don't know it.

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written by Devon Ryan Devon Ryan

yes you all right thank you, actually i pasted different columns from merged.gtf resulted by cuffmerge to use as a bed contains gene name, start, end for using in biophysconnector package for binning the reads are being mapped on genes

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written by zizigolu zizigolu

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