Comments (5)
cjfields
commented on August 22, 2024
2
The
check_samplesheet.pyscript has been already updated to get this information indevin #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.
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JoseEspinosa
commented on August 22, 2024
1
The check_samplesheet.py script has been already updated to get this information in dev in #349 but the IDR is not yet implemented.
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JoseEspinosa
commented on August 22, 2024
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
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cjfields
commented on August 22, 2024
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.
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cjfields
commented on August 22, 2024
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
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