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Hi after running ORFquant i got all the expected output files ex. gtf file, fasta file, final results file and tmp file but pdf/html reports not produced.
When i tried producing using the ORFquant …
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**Use case**
We are trying to use input normalized chip data to call peaks.
I see that probably the 'proper' way to do this is to simply use callpeak function with chip and input bam files, but we w…
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Hi @taoliu ,
**Describe the problem**
```callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B --SPMR -t TF.bam -c IgG.bam -n TF```
generate TF.narrowPeak files contain 6 rows.
```callpeak --…
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Hello, I am trying to export to the BedGraph File.
However, I only receive tag cluster file not divided into two strands.
This is what I did
```
> trk humanS_cluster |> CTSSnormalizedTpmGR(…
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Hi, I'm doing the differential loops analysis by `Imp_Scripts/DiffAnalysisHiChIP.r` And It went error after I just switched the positions of the input files in my execution script.
```{shell}
Rscri…
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Hello,
Great paper and great tool and thank you to sharing your docker environment to facilitate the use of your tool,
Maybe i'm doing something wrong, but when i'm trying to use `atacworks deno…
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### Have you checked the docs?
- [X] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [X] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules)
### …
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Hello!
Would it be possible for MAAPER to output a bedgraph file for all the genes with multiple PAS in each of the conditions separately? I would be interested in visualising the coverage track fo…
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I was able to generate the required bedGraph files and successfully create the R4Cker object. However when I run the nearbaitanalysis I get error message below:
[1] "Building adaptive windows..."
Err…
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I need to use deeptools to analysis my bulk ATAC-seq data. However, deeptools require a bigwig (.bw) file for most of the analyses.
I have tried two pipelines to generate bigwig file.
Pipeline 1:
…