Dear All,
I would like to download GRCh38-lite.fa and all_sequence.fa file for the hg38 version to run an analysis pipeline for whole exome sequencing data.
I have used the following for hg19 version for the same. But I cannot find a similar for the hg38 version.
Could someone help me with finding the files? Thank you.
What you are looking for is "Primary" assembly file.
Primary assembly contains all toplevel sequence regions excluding haplotypes and patches. This file is best used for performing sequence similarity searches where patch and haplotype sequences would confuse analysis.
You can find those sequences here at Ensembl (large download) or NCBI (large download).
NCBI sequence contains the following:
GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
A gzipped file that contains FASTA format sequences for the following:
1. chromosomes from the GRCh38 Primary Assembly unit. Note: the two PAR regions on chrY have been hard-masked with Ns. The chromosome Y sequence provided therefore has the same coordinates as the GenBank sequence but it is not identical to the GenBank sequence. Similarly, duplicate copies of centromeric arrays and WGS on chromosomes 5, 14, 19, 21 & 22 have been hard-masked with Ns (locations of the unmasked copies are given below).
2. mitochondrial genome from the GRCh38 non-nuclear assembly unit.
3. unlocalized scaffolds from the GRCh38 Primary Assembly unit.
4. unplaced scaffolds from the GRCh38 Primary Assembly unit.
5. Epstein-Barr virus (EBV) sequence Note: The EBV sequence is not part of the genome assembly but is included in the analysis set as a sink for alignment of reads that are often present in sequencing samples.
Based on what you wrote above:
GRCh37-lite is a subset of the full GRCh37 human genome assembly (assembly accession GCA_000001405.1) plus the human mitochondrial genome reference sequence (the "rCRS") from Mitomap.org. This set of sequences excludes all the alternate loci scaffolds of the full GRCh37 assembly, and has the pseudo-autosomal regions (PARs) on chromosome Y masked with Ns. This haploid representation of the genome is provided as a convenience for use in alignment pipelines that cannot handle the multiple placements expected in the PARs and in regions of the genome that are represented by the alternate loci.
this is the file you are looking for.
If you need the "all_sequences" i.e. including alt haplotypes then you should get the full sequence file from NCBI.
Note: Don't go on the fact hg38 files are not called lite or full. If you need those other viral sequences in new file then append them to the hg38 reference.
You can get them from accession numbers listed below or from your GRCh37-lite file.
GRCh37-lite-+-HPV_Redux-build consists of GRCh37-lite appended with a nonredundant subset of common human papilloma viruses. Included are HPV types 1 (NC_001356.1), 2 (NC_001352.1), 4 (NC_001457.1), 5 (NC_001531.1), 6 (NC_001355.1), 7 (NC_001595.1), 9 (NC_001596.1), 10 (NC_001576.1), 16 (NC_001526.2), 18 (NC_001357.1), 26 (NC_001583.1), 31 (J04353.1), 32 (NC_001586.1), 33 (M12732.1), 34 (NC_001587.1), 41 (NC_001354.1), 45 (EF202167.1), 48 (NC_001690.1), 49 (NC_001591.1), 50 (NC_001691.1), 53 (NC_001593.1), 54 (NC_001676.1), 60 (NC_001693.1), 61 (NC_001694.1), 63 (NC_001458.1), 88 (NC_010329.1), 90 (NC_004104.1), 92 (NC_004500.1), 96 (NC_005134.2), 101 (NC_008189.1), 103 (NC_008188.1), 108 (NC_012213.1), 109 (NC_012485.1), 112 (NC_012486.1), 116 (NC_013035.1), 121 (NC_014185.1), 128 (NC_014952.1), 129 (NC_014953.1), 131 (NC_014954.1), 132 (NC_014955.1), 134 (NC_014956.1), and 148 (NC_014835.1).
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version 2.3.6
What are the chromosomes inside those two files ? Is
liteprimary alignment ?Can you copy to output of :
Sorry, my question is about where can I find the
GRCH38-lite.fato download. I do not have it downloaded yet. I have onlyGRCH37-lite.faif you are asking me to grepGRCH37-lite.fa. Then this is how it looks like,What are the chromosomes inside those two files?
DNA chromosomeIs lite primary alignment?yesDescription from the README of
GRCH37-lite.fa:The header
And the
grep "^>" all_sequences.fa | headlooks as the following:Yes I meant GRCh37-lite.fa sorry,
I want the list of all entries in these files, just remove the
headin your command pleaseIf you only want primary assemblies you can take this one :
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/GRCh38.primary_assembly.genome.fa.gz
From : https://www.gencodegenes.org/human/
Thanks for the links. It is a big file. Do you want me to copy all lines here?
The lines are more than 5000 could you please tell me where should I post it or upload them?
5000 lines means 5000 chromosomes, alternatives, unplaced... That is a lot, I do not understand the difference between your 2 files
Could you try this :
grep -c "^>" GRCh37-lite.fa84
grep -c "^>" all_sequence.fa123
grep "^>" GRCh37-lite.fa | tail -10grep "^>" all_sequences.fa | tail -10You told me there were 5000 lines in your output in last message, I just see 84 and 123 count there... 84 entries should be 24 chromosomes + some unplaced/unlocated chromosomes so the file
GRCh37-lite.fais what is called primary file for GRCh38, the link I sent to you will be good.I do not know what is inside
all_sequences.fa, where did you download this one ? Seems like you have some viruses in thereThe README looks like this
I downloaded it from :
ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/