Sequences alignment

[FRANCISCO RODRIGUEZ MARTIN]

Good morning,

I have a question regarding RNA-seq repetitive sequences analysis. I would like to know if I can use UCSC GRCh38 repeatmasker annotation files to quantify reads aligned against GRCh38 ensembl human reference genome using STAR aligner.

Thanks for your attention,

Francisco

[Luis Nassar]

Hi, Francisco.

I'll preface by saying this is not our area of expertise. You may find better answers from people more familiar with STAR and repeats in Biostars (https://www.biostars.org/) or perhaps directly from STAR (https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf).

That said, we believe that in order to do this, you may first have to convert the repeat annotations to GTF and make the names unique for STAR.

Once we know the exact details, we can help you set up the repeat masker file from our own. Feel free to send us any Biostars replies on the topic or any further clarifying questions, and we'll assist as best we can.

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Lou Nassar
UCSC Genomics Institute