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sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)
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BAM files for gene expression analysis #29

Closed JillAshey closed 2 years ago

JillAshey commented 2 years ago

@yaaminiv @sr320 Where are the HISAT2 code and/or BAM files for the RNASeq gene expression analysis located?

sr320 commented 2 years ago

check out https://robertslab.github.io/sams-notebook/2022/01/31/RNAseq-Alignment-C.virginica-Adult-OA-Gonad-Data-to-GCF_002022765.2-Genome-Using-HISAT2-on-Mox.html

sr320 commented 2 years ago

There are links there that walk you back eg https://robertslab.github.io/sams-notebook/2021/07/20/Genome-Annotations-Splice-Site-and-Exon-Extractions-for-C.virginica-GCF_002022765.2-Genome-Using-Hisat2-on-Mox.html

sr320 commented 2 years ago

Looks like BAMs are at https://gannet.fish.washington.edu/Atumefaciens/20210726_cvir_stringtie_GCF_002022765.2_isoforms/

sr320 commented 2 years ago

BUT this might be what you are looking for https://github.com/sr320/ceabigr/issues/15

sr320 commented 2 years ago

@JillAshey are these in hand? can we close this issue?