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In GitLab by @ManavalanG on Apr 6, 2021, 08:45
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I believe that fastp would improve the current align-DNA pipeline and workflow.
fastp is an all-in-one FASTQ preprocessor. It performs read filtering, base correction, quality control, and adapter …
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Before running the sol GS pipeline, mixed model analysis, or GWAS a decision needs to be made about which trials and which plots should be used for a given trait. For example, before I run the sol GS …
ch728 updated
3 years ago
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This is to discuss the work that will need to be done to update 'has input', 'has output', and 'transports or maintains localization of' in GO-CAM models to 'has primary input' and 'has primary output…
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There is a slight shift in the GT segmentations of PSIR and STIR contrasts of the `canproco` dataset. We used these shifted segmentations in training the contrast-agnostic [model v2.4](https://github.…
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Dear developers,
Firstly, I would like to express my appreciation for the detailed ATAC-seq pipeline that you developed. As a PhD student, I find this tool extremely helpful in analyzing ATAC-seq d…
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Hi,
I changed the default reads that were used (some rerun). And rerun the QC.
But it seems that the name of analysis is not changed.
Just to ensure that the files/version of the reads that are us…
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Hi,
When trying the Pipecraft v.1.0.0 NextITS workflow I get the following error messages:
```
N E X T F L O W ~ version 23.04.1
Launching `/scripts/NextITS/Step2_AggregateRuns.nf` [admiring…
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Thanks for the great tool. I asked about this at ISMB, but would it be possible to also output either SAM (ideally to a pipe) or BAM files either in place of or in addition to the methylation metrics?…
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Hi Ivo,
I attach here the pipe and the screeshots of the errors.
(1) GATK_covariate_analysis: seems to me that the flag is correct (I double
checked on the website). The flag is working well i…