Generate reference index files for new STAR version

icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing

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Generate reference index files for new STAR version #435

Open edsu7 opened 6 months ago

guanqiaofeng commented 6 months ago

  May 10 13:29:08 ..... started STAR run
  May 10 13:29:09 ..... loading genome

  EXITING because of FATAL ERROR: Genome version: 2.7.1a is INCOMPATIBLE with running STAR version: 2.7.10a
  SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a

  May 10 13:29:09 ...... FATAL ERROR, exiting

edsu7 commented 5 months ago

In progress.

guanqiaofeng commented 3 months ago

STAR   --runMode genomeGenerate      \
--runThreadN 1   \
--genomeDir /data/reference_genome.index_STAR   \
--genomeFastaFiles /data/GRCh38_Verily_v1.genome.fa data      \
--genomeSAindexNbases 9   \
--sjdbGTFfile /data/gencode.v40.chr_patch_hapl_scaff.annotation.gtf   \
--sjdbOverhang 100

edsu7 commented 3 months ago

Following completion, upload onto resources folder in RDPC

guanqiaofeng commented 3 months ago

Available at ubuntu@10.30.134.105 /home/ubuntu/transcript_fa @lindaxiang

gen_transcript_fa_fai.py
GRCh38_Verily_v1.gencode_v40.transcriptome.fa.fai
GRCh38_Verily_v1.gencode_v40.transcriptome.fa

guanqiaofeng commented 3 months ago

Available at ubuntu@10.30.134.105 /home/ubuntu/star_index/GRCh38_Verily_v1.STARindex.sjdbOverhang_75 @lindaxiang

exonGeTrInfo.tab
geneInfo.tab
transcriptInfo.tab
exonInfo.tab
sjdbList.fromGTF.out.tab
chrStart.txt
chrNameLength.txt
chrName.txt
chrLength.txt
sjdbList.out.tab
sjdbInfo.txt
genomeParameters.txt
Genome
SA
SAindex
STARindex.log