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When I type hisat2-build in the hisat2 directory, it doesn't work for me and shows this error:" /usr/bin/env: ‘python’: No such file or directory"
While I can run hisat2 easily, hisat2-build doesn'…
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Hi,
I am facing issue with error 137 in case of Hisat2 version 2.2, while hisat2 older version 2.1 run successfully on my workstation with 128 GB RAM. I used hisat2 for rnaseq mapping with human geno…
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5' mismatch trimmer `trim_5p_mismatch.py` works with hisat2 output and bowtie output but not with default STAR output, because of differences in flags in the SAM file.
Currently, `trim_5p_mismatch.…
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Version: 1.4.8
RNAsik fails to run if bwa or hisat2 are missing, even if run won't use them based on the given commandline parameters.
eg, if `-align star` is specified, don't check for the exis…
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hello,
I could not use the automatic install , so I follow the set-by-step install
thinks looked ok, except for fastq-dump
I installed this:
curl http://data.biostarhandbook.com/sratools.sh …
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Hi,
We ran `HISAT2` (2.0.4) on a 422 sample dataset against hg19, then against hg38. Then using `featureCounts` we built some count matrices and analyzed them for differential expression and got ve…
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Hi,
As per the published hisat2/stringtie protocol, hisat2 is used with paired-end reads. I was wondering if hisat2 can be run using paired-end and singleton/single-read files together using -1, -2…
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Investigate the performance of parallelable tasks (those can run with more than 1 thread, controlled by `num_process`) under dataset `Wallace_2020_JEC21` and dataset `Woolstenhulme_2015`.
The tasks…
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Hi,
I am trying to extract SNPs using hisat2_extract_snps_haplotypes_VCF.py script from Ensembl VCF file (ftp://ftp.ensembl.org/pub/release-87/variation/vcf/danio_rerio/Danio_rerio.vcf.gz) to build…
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Hi there, I'm trying to run doctor.py to check the installation
~/bin/doctor.py
I get this message:
$ ~/bin/doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa …