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Hi @chbe-helix，
I hope this find you well.
When trying to repeat the tutorial HLA typing results with ILMN/NA12892 sample, I got the outputfile named "assembly_graph-hla.NA12892_extracted_1_fq…
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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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Hi,
I am working on starting a nextflow pipeline (v24.04.3) which among many other programs makes use of HISAT2 (v2.2.1) from a singularity container (v3.11.1).
During the execution of the pipe…
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Hi,
Thanks for a great tool for the analysis of circRNA-seq. I quantify the circRNA-seq data with CIRIquant, but I do not know which of the following ways to construct the index for the circRNA-seq…
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Hi! I recently ran the pipeline and got an error where a *_summary.log file was not detected during the execution of HISAT2.
Brief background: I'm using a Prochlorococcus genome as input and RNAse…
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I would like to use KMA, but I use HISAT2 and cufflinks for the alignment and quantification. How can I implement KMA in this pipeline for intron retention detection?
Thanks in advance!
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Hi, developers
In the version 2.2.0, as you said, some repeats handling features have been added to the tool. It's great for me because I wanna do some repeats analysis with hisat2. But there're so…
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## Expected Behavior
Jobs execute in parallel
## Actual Behavior
Jobs executed in parallel but an expression evaluation error caused successful workflow steps to fail. This error tends to occur w…
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I am using hisat2 version 2.1.0.
Command i using -
1 - For indexing
hisat2-build /index/Hg38_new.fa HG38
2 - For alignment -
hisat2 -p 8 --dta -x HG38 -1 sample_1.fastq.gz -2 /sample_2…
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Hi there,
I tried to use MicroExonator to analyze my dataset. The program finished successfully with -np. However, Errors as shown below occurred when I used it for my data analysis with "snakemake…