Dear all,
I have downloaded the GRCh38 reference human genome in fasta format from the ftp.ncbi.nlm.nih.gov following the suggestions of this post and this. Now I need to generate a fusion genome thus I need the headers right. The headers of the GRCh38 are in this form:
>chr1 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38
>chr2 AC:CM000664.2 gi:568336022 LN:242193529 rl:Chromosome M5:f98db672eb0993dcfdabafe2a882905c AS:GRCh38
>chr3 AC:CM000665.2 gi:568336021 LN:198295559 rl:Chromosome M5:76635a41ea913a405ded820447d067b0 AS:GRCh38
[...]
>chrUn_GL000218v1 AC:GL000218.1 gi:224183305 LN:161147 rl:unplaced M5:1d708b54644c26c7e01c2dad5426d38c AS:GRCh38
>chrEBV AC:AJ507799.2 gi:86261677 LN:171823 rl:decoy M5:6743bd63b3ff2b5b8985d8933c53290a SP:Human_herpesvirus_4 tp:circular
May I ask what is the format of the header? What the individual fields refer to?
Thank you
•
written
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marongiu.luigi
2 answers
>chr1 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38
AC accession number https://www.ncbi.nlm.nih.gov/nuccore/CM000663.2
gi: ncbi global identfier https://www.ncbi.nlm.nih.gov/nuccore/568336023
LN: length
rl: Assigned-Molecule-Location/Type (chromosome, mitochondrial...)
M5 : md5 cheksum https://en.wikipedia.org/wiki/Md5sum
AS: assembly
AC: Locus identifier / Accession number at Genbank & NCBI
gi: GI number (sometimes written in lower case, "gi") is simply a series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.
LN: Length of the contig
rl: role in the assembly, (chromosome, unplaced, EBV decoy)
M5: MD5 checksum (file integrity)
AS: Assemby version
SP: Species
tp: probably type, indicates if linear or circular
Anyway, to keep things compact I always delete everything after the first whitespace prior to building a genome.fa or index.
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