HISAT index with ERCC
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?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Reproducing ERCC spike-in correlation from public cfRNA data
written by MJ Cho •
-
RNA seq alignment issue
written by Hashan •
-
Problems using ERCC spike-ins for normalization in DESeq2
written by manuel.fernandez •
-
ERCC normalization within DESeq2
written by Assa Yeroslaviz
-
Difference between HISAT2 grch38 and grch38_snp indexes
written by ScubaChris •
-
Help with rat RNA-Seq data with the HISAT-StringTie workflow
written by JackieMe •
-
Computer requirements for RNAseq alignment
written by n.lu •
-
Cannot merge BCF files with `bcftools` files because "Index required, expected .vcf.gz or .bcf file…
written by jespinoz •
-
How to filter huge VCF files for datamining?
written by jespinoz •
-
How to get VCF file into a data matrix form for machine-learning? (new to vcf files)
written by jespinoz •
