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sub-task of #2
- [ ] 5a. human DLPFC ATAC-seq CP vs. VZ (Geschwind Cell 2018; ATAC-seq)
- [ ] 5b. ROADMAP fetal brain chromatin states
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Thank you for providing very useful software.
I wonder if this software is suitable for bulk tissue ATAC-seq and RNA-seq.
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Chromap is indeed an ultrafast tool. Thanks for developing and this method.
However, I have encountered two problems when I using chromap with scATAC-seq data.
The first one is that when I analyze…
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Describe the bug
pipeline because javax.net.ssl.SSLException failed
OS/Platform
OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
Conda version: conda 22.9.0…
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1. [Integrating ChIP-seq with other functional genomics data](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5888983/pdf/ely002.pdf)
2. [2014-nature review-Identifying and mitigating bias in next-gener…
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- [x] mRNAseq DESeq2
- [ ] mRNAseq sleuth
- [ ] noncoding RNAseq
- [ ] WGBS
- [ ] ATAC-seq
- [ ] ChIP-seq
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Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines:
https://github.com/kundajelab/atac-seq-pipeline
https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P…
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Dear all,
I am trying to run your ATAC pipeline, launching the following script with qsub on our cluster:
************************ lc.sh ************************
source /abcd/conda.sh
conda …
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Hi,
when I tried to run caper with encode-atac-pipeline, I could see the job was submitted to the lsf system, but the job disappear immediately without any reports.
when I looked into the detai…