Mouse ERV database for RNAseq analysis

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4.0 years ago

pb11 ▴ 30

Hello All

I am looking for mouse endogenous retroviral (ERV) database for RNAseq analysis. I want to align my fastq file with this database to obtain only those reads that are specific for ERV location. I have found this website Repbase https://www.girinst.org/repbase/update/index.html , however it requires subscription. Does anyone know how to do this? May be some leads? about database and analysis?

Thanks a lot

Prit

RNA-Seq R alignment sequencing assembly • 1.2k views

ADD COMMENT • link 4.0 years ago by pb11 ▴ 30

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http://geve.med.u-tokai.ac.jp/ looks like a free option. See if it helps.

ADD REPLY • link 4.0 years ago by GenoMax 147k

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Thanks. I tried that, its basically fasta file.

ADD REPLY • link 4.0 years ago by pb11 ▴ 30

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You could align your data to this file (not sure what it contains) since that is what you originally wanted to do.

ADD REPLY • link 4.0 years ago by GenoMax 147k

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