hg19.p13 annotation files

Question

[deepthithomaskannan]

Hi all,

I downloaded hg19.p13(GCF_000001405.25) fasta files from here. Release date is June 2013.

I needed gene annotation files for my downstream analysis. When I checked the UCSC website, they have the first release hg19 (GCA_000001405.1). Release date Feb 2009 and all the associated files. If I use UCSC annotation files for the hg19.p13, will that be alright? I think it is good to use the latest release of genomes. Since hg19 has all the associated file we decided to use hg19 instead of hg38. Is an annotation file available for hg19.p13?

My downstream pipeline includes both CNA(bowtie) and RNA (tophat,cufflinks,cuffdiff)analysis.

Any suggestions?

Thank you,
Deeps

Answer 1

[Jeremy Leipzig]

Those patch numbers (p.13) don't affect the primary assembly. The sequence you actually use does not differ from hg19.p1 to hg19.p13.

That is why it's called a "freeze". Can you imagine the chaos that would ensue if the genomic sequence changed every few months?

Applying Patches To Grch Assembly

[PoGibas]

Just adding, that according to GRC patches are "a way for us to provide updated information for a particular region without changing the chromosome coordinates".

[deepthithomaskannan]

Thank you guys!!