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Titles:
- Managing bioinformatic software and pipelines
- How to do bioinformatics like a professional bioinformatician
- Reproducible and scalable bioinformatics for researchers
Prerequisite…
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With file names:
```
SRR1917137_GSM1635411_Ikaros_ChIP-Seq,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz
SRR1917139_GSM1635413_Brg1_ChIP-Seq,_proB_cells_Mus_musculus_ChIP-Seq_1.fastq.gz
SRR191714…
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I am implementing this microtest repository and am wondering what should be placed in the [data path] section in these code blocks:
required_input_files: [data_path]
ngs_input_files: [data…
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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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This issue was raised by @Feat-FeAR :
The internal annotations for human chips do not have linked scripts for re-generation. Additionally, there are other considerations to make:
- Many Agilent micro…
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This issue is to explore the overview of Bioinformatics
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Create a workflow for peak calling VISION ChIP-seq datasets that (as closely as possible) matches the ENCODE best practices pipelines. ENCODE pipelines are [here](https://github.com/ENCODE-DCC/chip-se…
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Hi, all,
I would like to know where I can know the default parameters. Take bowtie2 as an example. I checked encode_tast_bowtie2.py and also the atac.wdl. I discovered that:
In encode_tast_bowti…
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Hi,
This is a general question about the `-slocal` and `-llocal` parameters. I wonder under what condition would the callpeak function uses `-slocal` and when `-llocal` is used? Since I'm using ma…