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https://github.com/haibol2016/ATACseqQCWorkshop
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Bulk ATAC-seq needs a new field for library adapters.
Two features:
1. The adapters should be per-library, so the field will be implemented as part of Library model.
2. submission code for Bulk A…
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ATAC-seq pipeline exit if no mitochondrial reads are duplicated due to zero division error - see logfile:
File "/Users/christianschmidl/src/open_pipelines/pipelines/atacseq.py", line 359, in parse_du…
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## **Describe the bug**
When running the pipeline, the number of reads in the "Fraction of mitochondrial reads" table does not match the number of reads in some of the other tables. For example, on …
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Hi! Thanks for the cool tool!
When I start from estimated read counts from a different pipeline (STAR > featureCounts) should I provide Taiji with raw reads or should I normalise them somehow before …
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Hi,
Thanks very much for developing this useful tool!
I am plotting four tracks for ATAC-seq and RNA-seq data with one control and one treatment each (as below).
![图片](https://user-images.git…
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I've installed caper v=1.6.3 on md Anderson seadragon cluster, and after I've try caper init seadragon, it shows:
```
Traceback (most recent call last):
File "***/.conda/envs/encode-atac-seq-pip…
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Hello,
I am attempting to use MMARGE for analyzing ATAC-seq data from different strains of mice. I downloaded the SNP and Indel vcf files from the Mouse Genomes Project website and sorted them usin…
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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!
I tried to make snap object from my own aligned BED file by snaptools 1.4.3.
snaptools snap-pre --input-file=snaptools_input_sorted.bed --output-snap=out.snap --genome-name=mm10 --genome-size=…