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in chip-seq paired mode is not used for MACS2

4

I dug a bit into the logs and I noticed that even if the data are paired-end MACS2 is not in paired end mode. I am feeding the --peakCallerOptions "-f...

sunta3iouxos

continuation from #924, warnings.warn("fragmentSize.metric.tsv is empty, this sets

12

This is the error I encountered: ```bash ChIP-seq -d /mnt/c/AP01/bamSpikes -j 8 --local --useSpikeInForNorm --getSizeFactorsFrom genome --spikeinExt Chromosome --sampleSheet /mnt/c/AP01/bamSpikes/H3K36me3.tsv --windowSize 500 mm10_gencodeM19_spikes /mnt/c/AP01/bamSpikes/H3K36me3_chip_type.yaml mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ChIP-seq/internals.snakefile:71: UserWarning: fragmentSize.metric.tsv is empty, this...

sunta3iouxos

CI dag test

1

Using -q / --quiet on top of a dryrun would make parsing the proposed number of rules more straight forward and easier to replicate with changing versions of snakemake. (which...

WardDeb

AnnotatedResults_MACS2_sampleSheet/Filtered.results.*_withNearestGene.txt had only 'NA' for GeneID and GeneSymbol. Looks like the wrong columns in the input bed (AnnotatedResults_MACS2_sampleSheet/Filtered.results.*_withNearestTranscript.txt) were used.

rbrauning

DNA-mapping pipeline gets stuck at origFASTQ rule when using a custom cluster config yaml

4

Using the following command, I tried running the DNA-mapping pipeline using a customized cluster config yaml to circumvent issues with one node on our server: `DNA-mapping --DAG --trim --trimmerOptions '-a...

TobiasHohl

katsikora

- [ ] update outputs, DAGs and folder descriptions for workflows - [ ] section on common options? - [ ] add a cookbook/FAQ section - [ ] update example...

katsikora

bwa aligned bams aren't properly filtered because of this and just sym-linked

jeffhsu3

enable spikein GTFs for mRNA-seq featureCounts

2

We recently came across the issue where the spikein GTF as specified using createIndices is not considered when using featureCounts in the mRNA-seq pipeline.

dkoppstein

currently, `mincount` is hardcoded to 20, which might be too high for some cutNx experiments

katsikora