Index with unmasked or masked in HISAT2

Question

[sansan96]

Hello everyone,

I have a couple of doubts about the query source and the genome that I have to use to create an index to align with HISAT2.

The first is whether it is correct to build the index with a "top level" file from Ensembl Plants (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/plants/fasta/zea_mays/dna/) or use the one from NCBI (https://www.ncbi.nlm.nih.gov/genome/?term=zea+mays)

If the correct thing is to use any of the Ensembl Plants, which would be the most ideal?

1. Zea_mays.Zm-B73-REFERENCE-NAM-5.0.dna.toplevel.fa.gz 615M

2. Zea_mays.Zm-B73-REFERENCE-NAM-5.0.dna_rm.toplevel.fa.gz 123M

3. Zea_mays.Zm-B73-REFERENCE-NAM-5.0.dna_sm.toplevel.fa.gz 641M

Description:

'dna' - unmasked genomic DNA.

'dna_rm' - masked genomic DNA.

'dna_sm': masked genomic DNA.

Could you help me clarify my doubts please?

Answer 1

[GenoMax]

Use top level file.

See README more information about other files you are referring to.

[sansan96]

I have read that in masked genomes low complexity and repetitive regions of DNA are detected and replaced with 'N', do you suggest using unmasked?

Thank you for your comments.