snakepipes

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`--predictChIPDict` ran on projects without control samples gives a dictionary, in which controls as listed as quoted empty strings. Parsing this in ChIP-seq results in control samples being recognized as...

katsikora

- [ ] createIndices: drop 'gtf to files', use `gtfToGenePred` instead? (would be consistent with repoTrampoline) - [ ] take transcript2gene.txt as input to Salmon_Alevin ("genes_t2g") - [ ] drop...

katsikora

It seems pytests would require the use of ruamel yaml instead of pyyaml (#966) (at least if we want to keep generating all the data 'on the fly'). This seems...

WardDeb

spikeIn sampe scaling factor calculation discrepenses

2

I am getting different results using the multiBamSummary command on my local PC using the following command that I expected to be the same on the server side, and I...

sunta3iouxos

Currently, splitSampleSheet looks for a "batch" column, in addition to name and condition. Make it flexible, so that any column between name and condition might be included - so that...

katsikora

Error during DNA-Mapping workflow: bowtie2.index.err: No output file specified

2

Hi everyone, i am trying to analyse ATAC-seq data with snakepipes. Currently, I am facing an error during the DNA-mapping workflow. Before that, I have created an index for GRCm38....

jurummel

conda envs get re-created by another user of the same group

1

Some of the options to test: - [ ] add copying over of the env yml files to condaEnvDir (done by snakemake, not done by `snakePipes createEnvs`) - [ ]...

katsikora

ATAC example miss /bamCoverage/*.filtered.seq_depth_norm.bw files

5

I have installed snakepipes and downloaded ATACseq example for test run. However, the example does not run as I expected. I first run following the suggestion from command.sh and get...

HamletShaoE

difference in conda env hashes between snakePipes and snakemake

1

For rna_seq.yaml: name: snakepipes_RNAseq_environment_2.0 channels: - conda-forge - bioconda dependencies: # - python >= 3 - bedtools = 2.30.0 - samtools = 1.15.1 - subread = 2.0.1 - hisat2 =...

katsikora

no spikeIn chromosomes found with extention _spikein

12

Hi Katarzyna and everyone else, I can not run the spikeIns strings for Chip-seq, this is a CUT&RUN protocol that has the bacteria cary over that can be used to...

sunta3iouxos