Comments (5)
This one could be also relevant for the implementation of the IDR analysis specifically for ChIP-seq analysis, implemented in NF:
https://github.com/bioinfo-pf-curie/chip-seq
from chipseq.
We would need to think about how we define "replicates" here to use that right? Now that we have removed the replicate
column from the samplesheet. Maybe we can have an optional column for replicates
in the samplesheet for this kind of thing? 🤔
from chipseq.
Yes, that could be an option, another one could be to have a separate file with the information about replicates... In the case we want to keep the samplesheet standard across pipelines
from chipseq.
I did think about having a separate metadata file but why?! Keep it simple and have one would be my preference.
from chipseq.
Yes, I agree two metadata files means increasing at least 2x the possibility of making mistakes 😝
from chipseq.
Related Issues (20)
- Problem with samplesheet HOT 3
- Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1) HOT 3
- mergeBed ERROR: Requested column 10, but database file - only has fields 1 - 9. HOT 18
- Normalisation of bigwig files
- package or namespace load failed for ‘UpSetR’ HOT 3
- No Space left on device error HOT 3
- Make subworkflows & modules available for nf-core tools HOT 1
- Default values for p-value and FDR
- Get rid of checkIfExists for params paths
- minor "samplesheet_pe.csv" format issue
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model!
- Error with NextSeq trimming
- Error running the pipline test in the BWA index step
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3
- There are multiple files for each of the following file names
- Can't run if there is no control
- Improve website on parameters section Alignment Options for argument --save_unaligned
- IDR analysis
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from chipseq.