Hi,
Thanks for building such a useful one-stop pipeline.
I found a small bug in the prep_mappability.sh script, line 196:
CMD="grep $CHR $OUTD/$MER.bedGraph | awk '\$4==1 {print \$2,\$3}' > $OUTFN"
When the loop goes to chr1, this line will grep not only chr1, but also chr10-chr19. Same for chr2. It will lead to malformated mappability files.
I suggest change the code to:
CMD="grep '$CHR\b' $OUTD/$MER.bedGraph | awk '\$4==1 {print \$2,\$3}' > $OUTFN"
which can make it match exactly chr1.
Hi, Thanks for building such a useful one-stop pipeline. I found a small bug in the prep_mappability.sh script, line 196:
CMD="grep $CHR $OUTD/$MER.bedGraph | awk '\$4==1 {print \$2,\$3}' > $OUTFN"When the loop goes to chr1, this line will grep not only chr1, but also chr10-chr19. Same for chr2. It will lead to malformated mappability files. I suggest change the code to:CMD="grep '$CHR\b' $OUTD/$MER.bedGraph | awk '\$4==1 {print \$2,\$3}' > $OUTFN"which can make it match exactly chr1.Best Yang