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I was running the test data in a cluster environment.
I had to extend the memory limit for counts_from_SALMON in tests/settings.yaml:
```
execution:
submit-to-cluster: yes
rules:
cou…
-
/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/cgigas_uk_roslin_v1_genomic-mito.index \
-p 4 \
-1 ../data/F143n08_R1_001.fastq.gz \
-2 ../data/F143n08_R2_001.fastq.gz \
-S ../output/F143_cgigas.…
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### Description of feature
Here I attempt to break down the required/desired modules for each processing stage of the workflow:
### Pre-Processing
- [X] Quality Control (FastQC)
---
- [X] Cu…
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Dear egaffo:
I am sorry to bother you again.
I was running circompara2 on CentOS 7 using docker.
Here is my command : "docker run -u `id -u` --rm -it -v $(pwd):/data egaffo/circompara2:v0.1.2…
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I use hisat2_extract_snps_haplotypes_VCF.py to extract SNPs and haplotypes from a VCF. When I used the VCF file which extracted from samtools, it can ran successfully. But when I used the VCF file wh…
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hi,doctor
i encounter a problem when use hisat2 ,can you give me some advice
fisrt,i use hisat2 build index for a large genome : hisat2-build --large-index ,it doesn't report any error .
…
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Dear Felix,
Thank you so much for developing this great tool! I rely Bismark heavily for my research :)
Recently we developed a haplotype-resolved diploid human genome, where one copy is paterna…
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Hi,
I was trying to extract count matrix by `prep.DE`, but I was getting the error.
```
Error: Text file with sample ID and path invalid ()
```
This is the command I used,
```
$ …
-
I'm unable to build on MacOS 12.2.1. Getting numerous `error: expected unqualified-id`
Truncated output below.
```
In file included from hisat2_build_main.cpp:20:
In file included from /Appli…
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in HISAT2 v2.2.0 the hisat2_read_statistics.py infers the input read file format from the filename extension: after removing possible compression extension, it checks either "fq" of "fastq" and, if no…