Question: Updated Alignment of current refseq transcripts against hg19
0
gravatar for cruckert
6 weeks ago by
cruckert0
cruckert0 wrote:

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...

hg19 vep alignment refseq genome • 114 views
ADD COMMENTlink written 6 weeks ago by cruckert0
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 written 6 weeks ago by ATpoint14k

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

See the Use genePredToGtf with a downloaded genePred table

ADD REPLYlink written 6 weeks ago by h.mon24k
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