chipseq
chipseq copied to clipboard
nf-core
ChIP-seq peak-calling, QC and differential analysis pipeline.
Looks like it might be due to the image not being created properly from the website during the nf-core sync process because the same logo was created here: https://github.com/nf-core/chipseq/blob/nf-core-template-merge-2.4/docs/images/nf-core-chipseq_logo_dark.png
* Move `ANNOTATE_BOOLEAN_PEAKS` under `skip_peak_annotation` in modules.config * Update parameters table in changelog
Related to https://github.com/nf-core/rnaseq/issues/544
Hello, I have been trying to run the nextflow/chipseq pipeline but failed due to the following error: Error executing process > 'CHECK_DESIGN (design_combined.csv)' Caused by: Process `CHECK_DESIGN (design_combined.csv)` terminated with...
The test for chromap are failing with the exception below: ```bash Caused by: Process `NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK (SPT5_T0_REP1)` terminated with an error exit status (1) Command executed: macs2 \ callpeak \ --keep-dup...
As mentioned above, the `--preset chip` argument of `chromap` includes the removal of duplicates (`--remove-pcr-duplicates` set by the preset) and thus, the downstream `PRESEQ_LCEXTRAP` process fails with the following error:...
It would be nice to implement DANPOS2 (already present in the MNAseseq pipeline) or similar to the ChIPseq pipeline for those looking forward to checking nucleosome positioning from histone variants...
I am looking for the MACS2 p-value signal for every base-pair, similar to the bigwigs available from [ROADMAP](https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/) or [EPIMAP](https://epigenome.wustl.edu/epimap/data/observed/). Had a discussion with @JoseEspinosa and he thinks it may...
To whom it may concern the following is a suggestion that I brought up on the slack and we thought would be worth it to add to the repo. In...
