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Hi,
running
```
nf-core/slamseq v1.0.0
Container: singularity - nfcore/slamseq:1.0.0
```
leads to
```
Error executing process > 'gtf2bed (genes.gtf)'
Caused by:
Process `gtf2bed (gene…
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I am trying to run a slamseq pipeline using `test` profile, but it hangs with the following message:
```
ERROR ~ No such variable: Exception evaluating property 'reads' for nextflow.util.ArrayTupl…
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Dear Tobias,
When I checked the counts file, I saw that the length of a UTR reported by slamseq is different with its length reported on UCSC.
For example, see the A1BG in my count file and UCSC;
…
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Quick question/suggestion: is there a way to install hisat-3n via conda or plans to make a hisat-3n conda recipe? Would be very helpful for integrating into Snakemake alignment workflows
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Hi there,
I am trying to execute slamdunk with samplesheet, and I am running into a problem - the reads are not used correctly as an input.
If I run the pipeline with the name of the file it wo…
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**Create a global parameters list**
Terminology between pipelines and shared assets can differ. To help preserve shared content and familiarity between pipelines, subworkflows and modules, it would…
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Hi,
I am dealing with quant-seq data, and I was wondering if I should use "-e" or not, also can you explain the description of "-e" in the DOCS, "Deactivates NextGenMap’s SLAMSeq alignment setting…
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Hi! I am interested in using DUNK for a non-SLAMseq dataset. I have RNAseq data in which I am looking for RNA editing (including hyper-editing which yields heavily edited reads) by ADAR1/2 which manif…
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Hi Tobias:
In my experiment(1mM 4sU pulse for 30 min), before library construction, all the steps followed the standard protocol of SLAMseq, after total RNA extraction the rRNAs were removed from t…
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This is my command:
slamdunk all -r /home/ubuntu/data/hg38.fa -b /home/ubuntu/data/slamseq/hg38_3UTR -o /media/volume/slam_result -t 8 /home/ubuntu/data/trimfile/DMSO_8h_trim_rep1.fq.gz
then I c…