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Hallo all,
I was reading the pepatac publication and I read a bit their pipeline. I find it to be the most interesting and comlete pipeline for ATAC.
Since it is very tough to get the whole pipeline…
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Hi,
Have you tested if the model can be trained to infer DNase-seq signal from ATAC-seq?
Best,
Chang
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Currently, many new analytical needs have emerged in single-cell ATAC-seq. Why doesn't ArchR consider accommodating them?
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Hi,
I am trying to use msCentipede on a ATAC-seq time course series without success. I get an error when running a command like
python call_binding.py --task learn --protocol ATAC_seq testbk/Ctcf_…
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I have bulk ATAC-seq from two cell populations (two replicates each). Papers suggest for bulk counts to apply quantile normalization followed by GC bias normalization using CQN.
Does chromVAR acco…
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**Use case**
My data consist of BAM paired-end files already filtered by duplicates, mit reads, etc. (99% alingment)
**Describe the problem**
I tried to use this command in bash
macs3 hmmratac…
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I was trying to build my own genome, but it never finished running and did not create the tsv file. I allocated 80G and run it overnight and still not finishes.
Below are files that have been gener…
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### Description of the bug
Similar to #374 perhaps, I get a `Path value cannot be null` error when running `--aligner cellrangerarc`.
My sample sheet is:
```
sample,fastq_1,fastq_2,fastq_barcode,sa…
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Hello,
I've got a question. I would like to try your software to perform peak calling, but instead of using Chip-seq data I woul like to use it on ATAC-seq data.
Do you think it is possible? If so,…
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Hi,
I am trying the graph_peak_caller in ATAC-seq mode as you suggested in #8 . I am following the pipeline in vg to construct the variation graph. I worked on the mouse genome, in which case 21 gra…