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

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

rna-seq chip-seq
• 2,684 views • link
updated by Denise CS Denise CS • written by bxia bxia 
<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
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written by GenoMax GenoMax

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

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written by bxia bxia

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

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written by GenoMax GenoMax

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

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written by bxia bxia

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.

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written by GenoMax GenoMax

1 answer

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.

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written by Denise CS Denise CS

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