Dear Hisat group,
Thank you so much for posting such awesome algorithm. We are currently comparing all available algorithms for HLA typing.
We didn't find a official tutorial for HLA reference construction that's in detail. Let me know please if there's one that I missed.
I have however, followed the link that I occationally found.
https://hackmd.io/@linnil1/rkraXkHxF
I was able to install Hisat2, as well as downloading the uptodate HLA database.
mkdir hisat_index
cd hisat_index
wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat-genotype/data/genotype_genome_20180128.tar.gz
tar xvzf genotype_genome_20180128.tar.gz
wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38.tar.gz
tar xvzf grch38.tar.gz
rm grch38.tar.gz
hisat2-inspect grch38/genome > genome.fa
samtools faidx genome.fa
cd ..
mkdir -p hisat_index/hisatgenotype_db/HLA/
cd hisat_index/hisatgenotype_db/HLA/
wget -nd -mL ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/* -P fasta
wget -nd -mL ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/msf/* -P msf
wget ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/hla.dat
cd ../../..
Above are the exact code I used to acquire the database for genome and HLA Loci.
I have attempted to make a genotyping of my own data.
hisat_index="./hisat_index"
hisatgenotype --base hla
--threads 30
--keep-alignment -v --keep-extract
-z ${hisat_index}
-1 ${sample_name}.R1.fq.gz
-2 ${sample_name}.R2.fq.gz
--out-dir ./tmp_hisat
I have run the above code substituting into my own data. I have seen the exact log that was posted. However, I saw no result generated.
Also, I'd like to check if the index and or reference were successfully built. I looked into the "hisat_index" folder. A number of files were generated with names of "hla_backbone.fa", "hla_sequences.fa", "hla.snp", etc. They are however all empty.
I do not have the proficiency to check the coding. I look forward to receiving your reply.
All the best.
Field Tian
Dear Hisat group,
Thank you so much for posting such awesome algorithm. We are currently comparing all available algorithms for HLA typing.
We didn't find a official tutorial for HLA reference construction that's in detail. Let me know please if there's one that I missed.
I have however, followed the link that I occationally found.
https://hackmd.io/@linnil1/rkraXkHxF
I was able to install Hisat2, as well as downloading the uptodate HLA database.
mkdir hisat_index
cd hisat_index
wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat-genotype/data/genotype_genome_20180128.tar.gz
tar xvzf genotype_genome_20180128.tar.gz
wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38.tar.gz
tar xvzf grch38.tar.gz
rm grch38.tar.gz
hisat2-inspect grch38/genome > genome.fa
samtools faidx genome.fa
cd ..
mkdir -p hisat_index/hisatgenotype_db/HLA/
cd hisat_index/hisatgenotype_db/HLA/
wget -nd -mL ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/* -P fasta
wget -nd -mL ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/msf/* -P msf
wget ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/hla.dat
cd ../../..
Above are the exact code I used to acquire the database for genome and HLA Loci.
I have attempted to make a genotyping of my own data.
hisat_index="./hisat_index"
hisatgenotype --base hla
--threads 30
--keep-alignment -v --keep-extract
-z ${hisat_index}
-1 ${sample_name}.R1.fq.gz
-2 ${sample_name}.R2.fq.gz
--out-dir ./tmp_hisat
I have run the above code substituting into my own data. I have seen the exact log that was posted. However, I saw no result generated.
Also, I'd like to check if the index and or reference were successfully built. I looked into the "hisat_index" folder. A number of files were generated with names of "hla_backbone.fa", "hla_sequences.fa", "hla.snp", etc. They are however all empty.
I do not have the proficiency to check the coding. I look forward to receiving your reply.
All the best.
Field Tian