Update on Making and Mapping to a new reference transcriptome
- Concatenated fastq files from 4 individuals (over 200M reads) both sick and healthy.
- Digital normalization by kmer to make a smaller file size (8.7% of original size).
- Ran Trinity with really low max-memory and CPUs so that it would complete without crashing
- Predicted ORFs with TransDecoder.pl script.
- Evaluated contig stats to find that they were fewer, longer contigs.
- Mapped reads to this new assembly.
- Extracted read counts
- Assembled read counts table.
Differential gene expression analyses using DESeq2
Transfer the data files and the R scripts to your computer from the server. On Windows you can use WinSCP to drag and drop the files. On a mac, from a terminal window on your computer, navigate to where you want to put the files:
cd /place/where/you/want/the/files/on/your/computer/ scp youruserid@pbio381.uvm.edu:/data/project_data/DGE/* .The wildcard (“*“) grabs everything in that directory on the server and moves it to the present directory (”.“).
Let’s work through the script DESeq2_exploreSSW_trim.R script together…