Primary_assembly and GRCh38.84.gtf.gz are the files for mapping?

Question

[bxia]

Just start to learn, need to confirm this:

Primary_assembly (reference genome) and GRCh38.84.gtf.gz (annotation) are the files for mapping alignment reads?

does sm_Primary_assembly also work?

Have read some tutorial but just want to confirm I am doing the right thing.

Thanks

[GenoMax]

<sequence type>:
 * 'dna' - unmasked genomic DNA sequences.
  * 'dna_rm' - masked genomic DNA.  Interspersed repeats and low
     complexity regions are detected with the RepeatMasker tool and masked
     by replacing repeats with 'N's.
  * 'dna_sm' - soft-masked genomic DNA. All repeats and low complexity regions
    have been replaced with lowercased versions of their nucleic base

[bxia]

So the Primary_assembly is the reference genome, I don't need to download the entire GRCh38 project files, right?

[GenoMax]

Yes and probably no (not sure what you mean by GRCh38 project files).

[bxia]

The GRCh38 download link from illumina igenomes website, total files are about 14.2 Gb

[GenoMax]

That bundle includes pre-made indexes for bowtie v.1, bowtie v. 2.and bwa. You could get that bundle and save yourself the time of building your own indexes.

Answer 1

[Denise CS]

Primary assembly contains all chromosomes plus unplaced (and unlocalised) scaffolds. It does not contain patches and haplotypes. As @genomax2 already explained sm means soft masked, where regions of low complexity, such as repetitive regions, are in lower case. This is all explained on the README of our FASTA files from our FTP site.