Reference Genome Option for Star

yanailab / celseq2

Generate the UMI count matrix from CEL-Seq2 sequencing data

https://yanailab.github.io/celseq2/

BSD 3-Clause "New" or "Revised" License

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Reference Genome Option for Star #32

Closed tbeaux18 closed 4 years ago

tbeaux18 commented 5 years ago

Hello,

I am trying to use your entire pipeline but with the STAR aligner. However, I am unable to use it due to no variable that holds the reference genome path to map against in the config.yaml file.

Can there be a fix for adding the reference genome path?

Puriney commented 5 years ago

@tbeaux18 Hello, could you use the command by 'celseq2' to initiate a template for config.yaml?

$ new-configuration-file -o /path/to/wonderful_CEL-Seq2_config.yaml

You would be able to see these lines to specify path to genome.

## What is the absolute path to the command STAR?
STAR: '~/bin/STAR'
## Where is the directory to save STAR index?
STAR_INDEX_DIR: '~/ref/human/aligner_index/star/Ensembl/GRCh38/release_97'