RNA sequencing Feed switch- Liver and Gut

Source: Gareth Gillard. (24 June 2016)

TO DO : Library preparation- Tom and Gareth

File types: Raw counts from HTSeq-count - .counts.txt CPM - .CPM.txt log2 scaled CPM - .log2CPM.txt FPKM - .FPKM.txt log2 scaled FPKM - log2FPKM.txt The scaled counts (CPM, FPKM) are derived from the raw counts, and used TMM normalised effective library sizes (using edgeR functions).

For feed switch experiment:

Count tables, separated for liver and gut tissue (can alter sample separation at any point) /mnt/SeqData3/GenoSysFat/processed_salmon_feed_switch_data/count_tables

Script for counts /mnt/SeqData3/GenoSysFat/processed_salmon_feed_switch_data/salmon_feed_switch_count_tables.Rmd

For liver slice experiment:

Count tables, with all liver slice samples /mnt/SeqData3/GenoSysFat/processed_liver_slice_data/count_tables

Script for counts /mnt/SeqData3/GenoSysFat/processed_liver_slice_data/salmon_liver_slice_count_tables.Rmd​

Raw sequence data: /mnt/SeqData3/GenoSysFat/Rawdata/160601_D00132.A.Project_Sandve-RNAlibs4-2016-04-26

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Created: 31st May 2016 at 13:10

Last updated: 20th Aug 2021 at 12:19

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