gravatar for javanokendo

2 hours ago by

University of Cape Town

How can I convert for example output from STAR aligner to junction.bed which is similar to the tophat junction.bed output. I have tried the following code but it does not work: awk {'if($4=="2") print "chr"$1"t"$2-$9"t"$3+$9"tJUNC000"NR"t"$7+$8"t-t"$2-$9"t"$3+$9"t255,0,0t2t"$9","$9"t","0,"$3-$2+$9; else if($4=="1") print "chr"$1"t"$2-$9"t"$3+$9"tJUNC000"NR"t"$7+$8"t+t"$2-$9"t"$3+$9"t0,0,255t2t"$9","$9"t","0,"$3-$2+$9'} $file >> $junction.bed but this till is not giving the bed file.
Kindly assist

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