GTF annotations

[FRANCISCO RODRIGUEZ MARTIN]

Good afternoon,

I write to you because I would like to know if all the tracks related to GRCh38 reference genome (specially the repeatmasker track) are compatible with this GRCh38 ensembl reference genome: https://ftp.ensembl.org/pub/release-114/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz. I am thinking about it because I want to perform RNA-seq analysis and I want to be sure that I can use these annotations files to quantify reads.

Thanks for your attention,

Francisco

[Gerardo Perez]

Hello, Francisco.

Thank you for your interest in the Genome Browser and for sending your inquiry.

Could you let us know which aligner you are using?

We recommend reviewing the aligner’s documentation, as the authors often suggest the most appropriate genome assembly version to use. For example, if your aligner doesn’t support _alt or _fix sequences, including them in the FASTA file can negatively impact alignment by diverting good reads away from the primary chromosomes.

You may find the Analysis Set section of the README file in our downloads directory helpful:
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/README.txt

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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