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singleron-RD / CeleScope

Single Cell Analysis Pipelines
https://www.singleron.bio/
MIT License
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celescope rna mkref but no folder output #280

Closed CaiCheng1996 closed 7 months ago

CaiCheng1996 commented 7 months ago

Describe the bug Run mkref to make my own index: celescope rna mkref --genome_name Sugarglider_Genome --fasta sugarglider.fasta --gtf sugarglider.gtf --thread 12

A lot of outpu files but no folder named "Sugarglider_Genome" that I want like cellranger. Output includes:(Too many useless files, it's really terrible) celescope_genome.config chrLength.txt chrNameLength.txt chrName.txt chrStart.txt exonGeTrInfo.tab exonInfo.tab geneInfo.tab Genome genomeParameters.txt Log.out SA SAindex sjdbInfo.txt sjdbList.fromGTF.out.tab sjdbList.out.tab transcriptInfo.tab

Chenjunjie1996 commented 7 months ago

You can manually create Sugarglider_Genome folder.

  1. mkdir Sugarglider_Genome
  2. cd Sugarglider_Genome
  3. celescope rna mkref --genome_name Sugarglider_Genome --fasta sugarglider.fasta --gtf sugarglider.gtf --thread 12
zhouyiqi91 commented 7 months ago

The mkref command generates the genome index file in the current directory. You can rename the directory where you run the mkref command to Sugarglider_Genome and then provide the path to this directory to the --genomeDir parameter when running the rna pipeline.