HelikarLab / FastqToGeneCounts

This is an automated pipeline to map SRR files to gene counts

https://helikarlab.github.io/FastqToGeneCounts

HelikarLab/FastqToGeneCounts Issues

Include documentation on how to set up a configuration file
Updated 8 months ago
Error in `fasterq_dump`
Updated a year ago
temp directory should not be named "scratch"
Closed a year ago1
validate.py throws error if missing REFLAT, BED or RNAINT_LIST, even if they are not necessary given the config.yaml settings
Closed a year ago1
Cannot handle certain combinations of desired outputs in config file
Closed a year ago
Rule contaminant screen race condition
Closed a year ago
Contaminant screen error
Closed a year ago2
Contaminant Screen fails with race condition
Closed a year ago1
Convert all "S" instances (single-end) into "SE" to reduce confusion when using single-cell abbreviations in the future
Updated 2 years ago
Test single cell alignment against known results
Updated 2 years ago
Include single-cell alignment into `rule star_align`
Updated 2 years ago
Trimming leaves adapter sequences longer than 90 base pairs
Updated 2 years ago
Contaminant Screen missing input
Closed 2 years ago2
MultiQC Extra Folderes
Updated 2 years ago
Snakemake --profile slurm --dry-run showing AttributeError
Closed 2 years ago1
Add Conda Channels during Installation
Closed 2 years ago1
Results directory missing
Closed 2 years ago
Reference Genome Documentation
Closed 2 years ago
Snakemake Version
Closed 2 years ago
Update Wiki
Closed 2 years ago1
snakemake install instructions
Closed 2 years ago
Update cookiecutter profile installation
Closed 2 years ago2
Installation Script
Updated 2 years ago