Comments (5)
The
check_samplesheet.py
script has been already updated to get this information indev
in #349 but the IDR is not yet implemented.
Yep, missed that. I definitely like having the explicit column for this better than the _r1
, _r2
convention.
from chipseq.
The check_samplesheet.py
script has been already updated to get this information in dev
in #349 but the IDR is not yet implemented.
from chipseq.
Actually, I just remembered that for the IDR analysis the replicate information would be needed in case this feature is implemented, see #235 and #87
from chipseq.
I'm not sure if there has been any input on this, but we have several ChIP-Seq projects that have biological reps, so having some way to keep track of these and perform IDR would be great.
from chipseq.
In the short term, couldn't replicates be captured when checking the sample sheet, then used downstream? Around this spot:
chipseq/bin/check_samplesheet.py
Line 80 in 51eba00
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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 HOT 2
- Get rid of checkIfExists for params paths HOT 1
- minor "samplesheet_pe.csv" format issue HOT 1
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model! HOT 2
- Error with NextSeq trimming HOT 2
- Error running the pipline test in the BWA index step HOT 2
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3 HOT 1
- There are multiple files for each of the following file names
- Can't run if there is no control HOT 2
- Improve website on parameters section Alignment Options for argument --save_unaligned HOT 1
- IDR analysis HOT 2
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