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Question: Updated Alignment of current refseq transcripts against hg19
1
Entering edit mode
9 months ago
cruckert • 10

I am in search for an alignment file of up to date (latest release is 92 from January 2019) refseq transcripts against hg19 genome in GFF/GTF format which I can use in Ensembl VEP as described in this post.

The latest alignment against hg19 provided by NCBI itself is from January 13, 2017 and misses many of the newer/updated transcripts: ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/

UCSC seems to have a newer alignment http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz but in table format which is not easily convertible to GTF format (the table browser itself uses an older version).

Does anybody know of other sources providing an up to date alignment?

Maybe it's time for hg38...

Entering edit mode
2

Maybe it's time for hg38...

It is, unless your project is has a legacy burden that forces you to stick with hg19. If not, I would switch.

ADD REPLYlink 9 months ago
ATpoint
17k
Entering edit mode
0

but in table format which is not easily convertible to GTF format

See the Use genePredToGtf with a downloaded genePred table

ADD REPLYlink 9 months ago
h.mon
25k

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