Converting SJ.out.tab from STAR aliner to junction.bed
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19 months ago

How can I convert for example T042BLSJ.out.tab 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"\t255,0,0\t2\t"$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"\t0,0,255\t2\t"$9","$9"\t","0,"$3-$2+$9'} $file >> $junction.bed but this till is not giving the bed file. Kindly assist

rna-seq alignment • 292 views
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