cannot get result when using hg19 ref for test bam

[houruiyan]

还有一个问题请教，想要创建hg19的ref，我准备了hg19的gtf fasta 文件，test bam是你的demo bam，也报错跑不通

[houruiyan]

Can you provide some detail to prepare the gtf and fasta file for hg19?

[aina91]

Ok, I use the hg19 reference genome file from 10X genomics, the same reference file required for Cell Ranger.
wget https://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz

[houruiyan]

Hello, this file is hg38. Please double check.

[houruiyan]

The demo bam file what I provided is based on hg38. You should also use the hg38 in the CamoTSS.
Please make sure to use the same reference file for both alignment and running CamoTSS.

GRCh38 is corresponding with the hg38. GRCh37 is corresponding with the hg19.

[aina91]

Oh, I apologize for the copy-paste error.
wget https://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz
Our current research is based on the hg19 reference genome, and it may be a good choice to switch to the latest reference genome version (e.g., upgrading from hg19 to hg38). The major advantage of this version is that it includes annotations for a greater number of known genes and non-coding RNAs, which helps us in accurately identifying and annotating novel transcriptional products. However, it is possible that we would need to update or re-run some analysis tools and workflows to adapt to the new reference genome.

[houruiyan]

I think there are two solutions:

1. try to rerun your alignment process by taking hg38 as reference and then do the next steps.
2. keep to run CamoTSS with the same reference genome of alignment (hg.19). Then try to use liftover.

[aina91]

Thanks!