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### Description of the bug
I am trying to process a dataset that consists of about 100 fastq files using the pipeline. I am running the pipeline on a HPC which is managed using Slurm. The first few…
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Due to questionable provenance of the alignment files uploaded previously to the publicly facing server, we have decided to re-map all RNA-seq samples described in the [summary table GSheet](https://d…
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### Description of the bug
Whenever I launch scrnaseq with `--aligner kallisto`, it crashes at the counting step with the following error message: `kb count: error: the following arguments are requir…
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Hi,
First of all: great tool to visualize the rearrangements!
It works all perfectly fine as long as I use Mummer for the alignment, and the .coords and .delta files. However, when I try to use…
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**command line**
`ragtag.py patch -u -t 32 --join-only j_h_read_trimming_gh.bp.p_u.purged.fa polished_contigs.fasta`
**log**
```
Wed Sep 21 10:19:47 2022 --- VERSION: RagTag v2.1.0
Wed Sep 21…
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[@aedera This is a followup to issue #29.]
I am experiencing problems when using AriocP with the encoding generated by the new build. It runs without throwing errors but it gets stuck during the ma…
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Hello everyone,
Thank you developing Sierra. I want to use it on some scRNA-Seq data but as I guess, the alignment step is crucial in this case. I believe STAR works fine in this case. Is it okay to …
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Hello,
I ran STAR version 2.6.1.a
When I try to run STAR-Fusion 1.5.0 with the Junction file using Docker, I have this error :
CMD: mkdir -p /data/Documents//_starF_checkpoints
CMD: mkdir -…
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Hi,
I ran the following using the star_index of the testdata (made by default run settings of STAR genomeGenerate)
`nextflow run nf-core/scrnaseq --reads 'data/S10_L001/*_R{1,2}*.fastq.gz' -pro…
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Hi there,
Just wanted to say great paper, its fantastic that you can push the throughput by optimizing the decrosslinking.
I am currently using Pore-C but adapted using DNase based method to fra…