trf2bed

[jaudall]

Is there a recommended or vetted output convert to make a bed file from the trf output?
e.g. trf2bed.py

I've found one online, not sure if works. Are there better ways?

[kfletcher88]

One-line awk solution:

awk -v OFS='\t' '$1 == "Sequence:" {fa = $2; next} ; NF == 15 {print fa, $1, $2}'

[Adamtaranto]

For the record, if anyone wants to convert a trf dat file to GFF3 you can use the TRF2GFF tool.