We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
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
-b
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 get the desired output.
-i
-x
It will be a great help if someone please correct me.
The text was updated successfully, but these errors were encountered:
No branches or pull requests
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,
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 indextime 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 get the desired output.It will be a great help if someone please correct me.
The text was updated successfully, but these errors were encountered: