converting txt to bed

Question

[zizigolu]

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

[Devon Ryan]

What you pasted looks like BED file already.

[h.mon]

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

Answer 1

[biocyberman]

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.

[zizigolu]

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

[Devon Ryan]

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.

[zizigolu]

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