Convert Bamtobed Score

Question

[Stevelor]

Hey,

just a short question....is there a possibility to set the score in the bed file to "1" an not to the the alignment score?? arguments -tag and -ed only use BAM alignment tags... ?!? :/

Cheers!

Answer 1

[Pascal]

I suggest you use awk after bamToBed. If the score you want to replace is in column 4 you could use:

cat your_file.bed | awk '{ print $1"\t"$2"\t"$3"\t1\t"$5"\t"$6}'

[Stevelor]

I was looking for a one-step-solution within this tool....so this is what i would do if bamToBed really can't use a defined value as score :/ Thanks!

[Pierre Lindenbaum]

or: awk '($4="1")'

[Pascal]

Whatch out Pierre: this trick doesn't output with tab-separated columns...