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### Description of the bug
I'm running nf-core/rnaseq with the following command:
```
nextflow run nf-core/rnaseq
-r 3.14.0 …
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I'm getting the following error:
```console
#### Aligning reads to genome using minimap2
02:20:30 AM Thu Apr 04 2024 minimap2_align
Warning: error in running command/home/rstudio/miniconda3/bin/…
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* spladder version: v2.4.2
* Python version: Python 3.8.5
* Operating System: Linux version 4.19.128-microsoft-standard (oe-user@oe-host) (gcc version 8.2.0 (GCC))
* Machine Configuration: 8 Cores(…
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Hi there,
I have an human ONT direct cDNA data that I would like to analyze using IsoformSwitchAnalyzeR. I have aligned it using ENSEMBL reference cDNA fasta and then ran alignment mode in salmon u…
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Hi , thanks for developing such a good tool.
and I run with the following command :
isoquant.py -d nanopore --bam /.bam --reference /GRCm39.genome.fa.gz --genedb /gencode.vM33.primary_assembly.basic…
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Hi
I am trying to use TAGADA to improve my annotation of a plant genome.
I input my draft annotation as a GTF file (v 2.2) and provided 40 BAM files of RNA-Seq I had previously aligned with HiSat…
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Hi,
I tried running a task with a memory limit of 250GB, but it kept going over the l…
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we have been running Isoquant, the reference-based mode on Pacbio sequenced SIRVs samples, and encountered an issue that 1. isoform reported all as novel isoforms, but we can find most of them match t…
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Hello again,
I opened a new issue as a followup to: https://github.com/TobiTekath/DTUrtle/issues/6#issuecomment-1124182002
In my csv file, I have barcodes as columns and transcripts as rows:
Tr…
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I have been running `iCount xlsites` to identify cross-link sites using read quantification in my eCLIP sample replicates for PEKA. I selected read quantification as the input BAM files have been UMI-…