Entering edit mode
14 months ago
kabir.deb
▴
90
Hi,
I'm trying to get a mappability wig file by running generateMap.pl
from hmmcopy_utils. However, I'm getting a message which states that,
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
What I did,
HMMCOPY_DIR=~/mysofts/hmmcopy_utils-master
REF=~/RefHu/btindx/GRCh38_chr.fa
index=~/RefHu/btindx
First, I created an index file using Bowtie,
time srun bowtie-build --threads 8 -f $REF $index/GRCh38_chr
time srun $HMMCOPY_DIR/util/mappability/generateMap.pl -w 10000 ${REF} --index $index/GRCh38_chr -o $index/GRCh38_chr.fa.map.bw
Again I used -b
for creating index
time srun $HMMCOPY_DIR/util/mappability/generateMap.pl -b ${REF} -o $index/GRCh38_chr.fa.map.bw
time srun $HMMCOPY_DIR/util/mappability/generateMap.pl ${REF} -o $index/GRCh38_chr.fa.map.bw
I also tried using -i
and -x
for index files but not getting the desired output.
It will be a great help if someone please correct me.