Question: HISAT index with ERCC
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gravatar for n.lu
6 days ago by
n.lu30
n.lu30 wrote:

Hi,

I'd like to align my RNA-seq data from Mus musculus, containing ERCC spike-ins with HISAT2. Because I lack computer power to build my own index, I plan to downlowd a prebuilt index from their site (ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/) and as far as I can tell the only one containing ERCC sequences (for Mm) is grcm38_snp_tran_ercc.tar.gz. The plan of my experiment was just to explore basic differential gene expression, so I am not interested in SNPs which are included in this index. Is ok to use it in this case?

rna-seq alignment hisat ercc • 48 views
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