cougarlj
commented
2 years ago Dear tkaraman19,
Based on my experience, you can fix it through two ways.
- You can build the index by yourself directly through STAR. The command like: STAR --runMode genomeGenerate --genomeDir /your/dir --genomeFastaFiles /your/fastq/file/hg38.fa . You should put the index directory in ***/bundle_v1/db//star/hg38
- When you run the alignment module for the first time, you can add the parameter "-mbi" and this will help you to build the index automatically. If it fails for some reasons I don't know, you can copy the command on the screen and run it independently to build the index directly.
If you have any questions, please let me know.
Best Wishes, Jiang Li
On Mon, Nov 29, 2021 at 4:24 PM tkaraman19 @.***> wrote:
Hi there, I followed the steps one by one, i am stuck with the star alignment part. It asks me to generate a genome index file and I dont know how to do it. Can u give me advice to overcome this. Thank you
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Hi there, I followed the steps one by one, i am stuck with the star alignment part. It asks me to generate a genome index file and I dont know how to do it. Can u give me advice to overcome this. Thank you