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Hi, I am tring to call peaks using macs2 from ATAC-seq data.
many papers use --shift -100 --extsize 200 for MACS2 rather than -f BAMPE; but my data is paired_end reads，if I use -f BAMPE, then the …
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- Move length and quality trimming in bonus exercises in QC practical to gain a bit of time (day 1 morning)
- Move ChIP-seq lecture in the morning of day 1
- This will give more time to go explain a…
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Single-cell/nucleus datasets typically contain matched FASTQ files, in groups of 2 for RNA-seq and some ATAC-seq assays, and 3 for other ATAC-seq data types. (RNA-seq contains 2 more files per group, …
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This is a question about the .table file. I understand that LIGER integrates the scATAC and scRNA-seq. What exactly does this .table contain, and how can I generate it from other pipelines (Seruat, sc…
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> cat PUMATAC_tutorial-main/PUMATAC/src/singlecelltoolkit/processes/barcode_correction.nf
nextflow.enable.dsl=2
//binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolk…
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## Figure files
https://drive.google.com/drive/u/1/folders/17ukhBF1y_acxglZtf8wsH4Hfw329q8-9
## Panel legends
- [x] a. 4673 snmC Cell cluster centroids tSNE colored by 261 cell sub-classes. Dots …
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https://doi.org/10.1101/172767 (http://www.biorxiv.org/content/early/2017/08/06/172767)
> Determining the binding locations of regulatory factors, such as transcription factors and histone modifica…
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I am facing following error while using macs14
**Command used** : macs14 -t test.bam -c control.bam
**Error**
# ARGUMENTS LIST:
# name = NA
# format = AUTO
# ChIP-seq file =text4.bam
# control file =…
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https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runMACS.R#L32
According to the [MACS2 page](https://github.com/taoliu/MACS) the settings
```--shift -100 --extsi…
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I just realized something on Pulsar:
This library is a snRNA library but it says ATAC at the bottom of the page (ATAC 320). This is not an urgent fix but I think it would be good to change this to RN…