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### Description of feature
As stated in the [10X docs](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-flex-multi-frp):
> Important: In the examples be…
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### Ask away!
The workflow completes but I'm not able to locate the alignment.bam file that is listed as one of the outputs. I've had the same issue running in EPI2me desktop and in the command line …
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Hi,
I conducted a test on a dataset and generated my BAM and BAI files using 'samtools'. However, I encountered some errors during the process. I would appreciate any solutions you might have. A…
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Hi,
We have 10x data from a cell village and I am trying to identify donors in the village using donor assignment. I have the 10x bam file, barcodes.tsv, gtf and vcf files.
Step 1: I ran Drop-seq…
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Hello
I have a question/issue regarding the polyA requirement. So far, I have been using BAM files that were aligned using the ISOSEQ pipeline. As part of this pipeline, polyA tails are trimmed (`…
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### Description of the bug
Hi,
I want to ask why I use latesest version, but my results is still macs2, not macs3.
Here is my command line:
```
nextflow run nf-core/atacseq -resume -c nextflow.conf…
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bam!
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We ran bwa-meth method, following the traditional method where we are converting a sam into a bam file using SortSam with picard tools and am encountering the following errors. Could you please advise…
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The function runs and creates the NucleosomeFree.bam, mononucleosome.bam, dinucleosome.bam, and trinucleosome.bam files, but these files only contain some header info. There are no actual alignment re…
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