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alexdobin / STAR

RNA-seq aligner
MIT License
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versionGenome issue / clarification #2065

Open kvn95ss opened 4 months ago

kvn95ss commented 4 months ago

Hello,

I'm trying to run this pipeline - https://github.com/sdparekh/zUMIs

The tool comes with a miniconda environment which includes the required packages, which includes STAR v2.7.3a. However, when I create a genome index using this version of STAR, the versionGenome shows up as 2.7.1a. The command used to generate the index is as follows -

/home/user/Downloads/STAR-2.7.3a/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 15 --genomeDir . --genomeFastaFiles ../grch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta --limitGenomeGenerateRAM 40000000000

Regardless whether I use the STAR from the miniconda environment or pulling the release from Github, the versionGenome is still 2.7.1a.

My questions are -

  1. Does this indicate that the oldest version of STAR compatible with the index is v2.7.1a?
  2. If I use STAR v2.7.3a with this index, will this cause any issues?
alexdobin commented 4 months ago

Hi @kvn95ss

The versionGenome in genomeParameters.txt defines backward compatibility: the earliest version of STAR that can be used to index the genome. v2.7.3a will work fine with this genome.