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README for ftp://ncbi.nlm.nih.gov/refseq/H_sapiens/historical/

Last updated: June 23, 2023

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This directory provides alignments and annotation for current
and historical RefSeq transcripts, including both replaced
and suppressed RefSeq transcript versions. Only "known" RefSeq
transcripts with NM_ or NR_ accession prefixes are included.

The data is comprised of alignments collected from current and 
previous annotation releases of the GRCh38 assembly, favoring 
the most recent annotation release for any given transcript 
accession.version. The set is then supplemented with alignments 
of older transcripts that were never annotated on GRCh38. The
alignments are then filtered to remove rare transcripts that
aren't aligned to the expected location for its gene to remove
some historical errors. 

Genome annotation in GFF3 format is then generated from the set
of all alignments. The GFF3 output differs from GFF3 provided as 
part of regular annotation releases by omitting use of short 
1-2 bp "microintrons" to represent indels. The annotation GFF3
is provided to indicate CDS locations on the genome, but 
remapping from transcript to genome coordinates should always 
rely directly on the alignment data.

Current annotation releases are named using the format:
<assembly acc.ver>-RS_YYYY_MM
The historical alignment set is anchored on the most recent 
annotation release.

Provided files:
1. GCF_000001405.40-RS_YYYY_MM_knownrefseq_alns.gff.gz
alignment files in GFF3 format
see: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/file-formats/annotation-files/about-ncbi-gff3/#alignments

2. GCF_000001405.40-RS_YYYY_MM_knownrefseq_alns.bam
   GCF_000001405.40-RS_YYYY_MM_knownrefseq_alns.bam.bai
alignment files in BAM format

3. GCF_000001405.40-RS_YYYY_MM_genomic.gff.gz
annotation files for the corresponding alignments