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RefSeq transcripts *.rna.fna.gz files

A very basic question:

What's the difference between the "*.rna.fna.gz" files at: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/

and "GRCh38_latest_rna.fna.gz" at: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/?

Are the RNA sequences in "GRCh38_latest_rna.fna.gz" exactly the same as the ones in the combination of all "*.rna.fna.gz"?

Thanks a lot!

sequence rna-seq
• 3,798 views • link
written by seqall • seqall

From what I can tell, the files in the directory ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/ are just symbolic links to data elsewhere on the NCBI servers, links that are updated such that they will always point to the most updated files.

GRCh38_latest_rna.fna.gz contains the mRNA sequence of all RefSeq transcripts, specifically:

grep -e ">" GRCh38_latest_rna.fna | cut -f1 -d "_" | sort | uniq -c
50052, NM
15544, NR
63555, XM
30847, XR

The files in the other directory are broken up into various chunks, for whatever reason, but the sequences in them are exactly the same as per GRCh38_latest_rna.fna.gz. According to the README files, these 'chunks' also contain all RefSeq transcripts

• 1 views • link
written by Kevin Blighe Kevin Blighe

Thanks a lot for your info, Kevin! After investigation and inquiry of this two sets, it turns out that the "*.rna.fna.gz" files at: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/ are the latest and contain newer versions of transcripts. They have mRNA sequences:

grep -e ">" human.all.rna.fna | cut -f1 -d "_" | sort | uniq -c
50102 >NM
15535 >NR
63532 >XM
30843 >XR

After comparing all the transcript IDs

grep -e ">" GRCh38_latest_rna.fna | cut -f1 -d " " | sort > refseq_ids_GRCh38_latest
grep -e ">" human.all.rna.fna | cut -f1 -d " " | sort > refseq_ids_human_all
diff refseq_ids_human_all refseq_ids_GRCh38_latest

A part of the differences are as follows:

41c41
< >NM_000054.5
---
> >NM_000054.4
83c83
< >NM_000097.6
---
> >NM_000097.5
468c468
< >NM_000500.8
---
> >NM_000500.7
1944,1945c1944,1945
< >NM_001008703.3
< >NM_001008704.3
---
> >NM_001008703.2
> >NM_001008704.2
• 1 views • link
written by seqall • seqall

Interesting. Perhaps feed this back to the NCBI (if not already done).

• 1 views • link
written by Kevin Blighe Kevin Blighe

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