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Hi,
I'm running this command:
```
CIRIquant -t 25 \
-v \
-1 alignment_rrna/13_S1_unmappedreads_1.fq.gz \
-2 alignment_rrna/13_S1_unmappedreads_2.fq.gz \
…
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**Snakemake version**
*snakemake-wrappers:* 3.3.3
**Describe the bug**
The wrapper looks for the index file checking for *.ht2* file extension only. So this fails when a *large* index was pr…
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hi guys i try to use hisat2 aligning the fastq file to the index which i have built before, here is the command line:
/home/wyf/miniconda3/bin/hisat2 -x /home/wyf/Pipeline/RNA-seq/02.hisat/Eriochei…
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Hi, I tried running the pipeline and got this error:
Killed
(ERR): hisat2-align exited with value 137
[E::aux_parse] Incomplete aux field
samtools view: error reading file "-"
samtools view: er…
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I have RNA-seq data from two conditions (control and splicing factor knockout) and would like to use the SpliSER tool to analyze differential splice site usage between these conditions. To do so, I ne…
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After indexing chromosome 20, Some of us keep receiving this error on attempting aligning:
**Warning: Could not open read file "/ngs/glucoma/SRR5858161_1.fastq" for reading; skipping...
Error: No …
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I try to run the pipeline with the testdata and singularity:
`nextflow run main.nf -profile test,singularity`
However, i get this error, although i have permissions to write/read to /tmp/.
``…
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Hello, I have tried this pipeline and found an issue with alignment; most of the reads were not aligned. Is it possible to get the HISAT2 CHM13v2 index files? Thank you so much.
Below is the code I…
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Hi Lasse,
This is similar to the request for STAR alignment support in bayesassembler. Is there anyway to give the program, HISAT2 alignments instead of Tophat2. Hisat2 as you know is the successor…
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bismark
the map command : /bismark --genome_folder ../01.hap1 --hisat2 --non_directional -1 ../clean_ZHM1H.R…