HG38 IS OK?

[SiyuanHuang1]

very nice work! But I have some questions about this pipeline:
1.hg38 is ok? Or It just depends on which one you used when you made alignment by cellranger pipeline?
2. what is the format about "chromosome length file" in the "configfile.txt" file? It is a .fai file? Can you give a demo?

[2019surbhi]

You can download chromosome length file for specific genome reference from UCSC or create your own for your specific reference using the code (requires Python):

faidx hg19.fa -i chromsizes > hg19_chr_sizes.

[jung233]

I also have the same problem; May I ask if you can provide detailed explanations of files such as hg19. introns.rda, hg19. utr. rda, so that I can replace them with GRCh38; Thank you very much.