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Is there a straightforward way to get strand information for the bedGraph or coverage files produced by Bismark, without generating a genome-wide cytosine report? I would like to avoid that for runtim…
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My end goal is to annotate a VCF file with mappability scores, but in spot checking annotations for some mutation sites with the UCSC Genome Browser, I noticed some inconsistencies. Specifically, I an…
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Hello,
Thank you for serving such a nice tool in advance.
I tried to upload bigwig files that were separated for forward and reverse strand. In case of reverse stranded bigWig files, they have n…
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Dear Adam,
I can run the test data smoothly with the script NXF_VER=20.07.1 nextflow run epidiverse/ewas -profile test,conda
But when I run the pipeline use input parameter with script NXF_VER…
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Hello,
I am new to modkit, so I may be asking silly questions. The bedgraph generated using `modkit pileup --bedgraph` generates bedgraphs with five columns. The format description at [UCSC](http…
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Hello,
I successfully run `daric normalize`, and I would like to run `daric runhmm`.
However, I do not know which files I should use for the `-f, --deltaPIS` parameter.
Namely, `daric normali…
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Right now, the `ArithmeticTrackView` provides binned data. It doesn't make much sense for sparse BedGraph-type files with identical structure, like the ones we use for miRNA expression data. Arguably,…
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`hicexplorer --version`
hicexplorer 3.7.2
`hicPCA -m in.mcool::/resolutions/500000 -f bedgraph -o pca1.bedgraph pca2.bedgraph`
ERROR:hicexplorer.hicPCA:Number of output file names and number of e…
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Hello, I'm wondering why there is a difference between the TAD separation scores stored in the *fdr_tad_score.bm file and those stored in the *fdr_score.bedgraph file. My understanding is that the sco…
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Dear Ramya,
I am producing bedgraph files from bam by using your script ( i modified the chr and i add it at the end cause my mapping files had only 1,2 etc instead of chr1, chr2 ) .
When i am tr…