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We've been using a very small subset of RNA-seq data for our tests. Rule blind_clustering, and now also deeptools bamCoverage (with the BPM normalization and strand filtering in RNA-seq), aren't...

Right, the snakemake [logger](https://github.com/vanheeringen-lab/seq2science/blob/0542a671d06f301d48a67a484cf21ad991affbf3/seq2science/cli.py#L364) can only pickup stderr OR stdout. We could redirect the stderr with [contextlib](https://docs.python.org/3/library/contextlib.html#contextlib.redirect_stderr), but also need to print it to the console.

That's it! I can recreate logs missing `Error in rule...` by canceling this test run: `seq2science run download-fastq --cores 2 --configfile tests/download_fastq/default_config.yaml` However, the following test run does have the...

fixed with #118

> Can user-provided enhancer regions contain promotor regions? Yes! If you wish, you can even remove promoters during ANANSE network with the `--exclude-promoter` flag. > Why not train the enhancer...

I double checked the code to be sure :) Starting from version 0.2, we include both promoters and enhancers by default (with the option to exclude them). So that picture...

without niceness and 1 cores: same issue

Angela ran `Binding` on the student server. I think it was something like this: ``` ananse binding \ -g GRCz11.fa \ -A GRCz11-GSM3396550.samtools-coordinate.bam \ -r GRCz11_raw.tsv \ -n 12 \...

_I think_ the issue was resolved by rerunning binding with the zebrafish motifs2factors, and adding this with `--pfmfile`. Expanding documentation on `--pfmfile` and `--pfmscorefile` would help here. (I'll add it...

I'd say yes! One output file, and `ananse view binding.h5` returns and overview of the contents (without spewing all out in one go). Then a sub command to get the...