chipseq
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nf-core
ChIP-seq peak-calling, QC and differential analysis pipeline.
This feature will be needed to implement the IDR logic that need information about the replicates to calculate the reproducibility of the peaks, see #87
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/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit Another implementation in NF: https://github.com/DoaneAS/atacflow ENCODE ATAC-seq Guidelines: https://www.encodeproject.org/atac-seq/ Amongst other...
### Description of feature Hello everyone, Here is a metro map draft for nf-core/chipseq. Feel free to give feedback on it and to modify it yourself if you feel like...
### Description of the bug Hello, I have a problem with TMP where the chipseq pipeline stops at process > PHANTOMPEAKQUALTOOLS with an error message: "No space left on device"....
### Description of the bug Hello, I just ran one of my test samples that works on v1.2.2, but not on v2 of the pipeline. The pipeline works perfectly but...
### Description of the bug Hi! It appears the ability to skip phantompeakqualtools has been left out. "skip_spp" is listed in the parameters on the [nf-core site](https://nf-co.re/chipseq/2.0.0/parameters) but there's no...
Hi, I found the chipseq pipeline will run forever even when error [reported!](url) The command used to launch the workflow was as follows: ``` nextflow run nf-core/chipseq --input design.csv --fasta...
-[nf-core/chipseq] Pipeline completed with errors- i'm install this pipline in our lab server.but it have a problem. i guess that it's because the network. I don't know if there is...
Hi. I have a Single End MiSeq Chipseq runs(single replicate). My `design.csv` is as follows ``` group,replicate,fastq_1,fastq_2,antibody,control A1_IP,1,A1_S1_L001_R1_001.fastq.gz,,, C1_TF_Ab,1,C1_S2_L001_R1_001.fastq.gz,,TF,A1_IP E1_IgG_control,1,E1_S3_L001_R1_001.fastq.gz,,IgG,A1_IP G1_H3K27Ac_Ab,1,G1_S4_L001_R1_001.fastq.gz,,H3K27Ac,A1_IP ``` I tried running peak-calling using your nf-core pipeline...
Greetings, While attempting to process some data via the [Nextflow CHIPSEQ workflow](https://github.com/nf-core/chipseq) recently, the Nextflow execution appears to become stalled at a specific point in a deterministic fashion (i.e. re-runs...
