search

alexchwong / SpliceWiz

SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.
Other
13 stars 8 forks source link

reference build step in splicewiz #27

Closed rezarahman12 closed 1 year ago

rezarahman12 commented 1 year ago

Hi Alex,

I've got a query regarding the use of an appropriate human genome fasta file. Should I use [Homo_sapiens.GRCh38.dna.alt.fa.gz] (https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.alt.fa.gz)?

Or do I need to use [Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz] (https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz) ?

I'm using the gtf file [Homo_sapiens.GRCh38.108.gtf.gz] (https://ftp.ensembl.org/pub/release-108/gtf/homo_sapiens/Homo_sapiens.GRCh38.108.gtf.gz).

I would highly appreciate your time and comment. Best regards Reza

alexchwong commented 1 year ago

Hi Reza,

The genome used should be the same as that used to align the BAM files. Usually, this is the primary assembly.

Alternates and haplotypes generally feature alternate alleles (e.g. SNPs, etc). These are more for mutation analysis rather than transcriptome analysis.

Alex

rezarahman12 commented 1 year ago

Thanks a lot Alex.