This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
The analysis involves processing 20 samples for a de novo metatranscriptomic assembly of crab and bacterial RNA.
The aim is to evaluate whether the bacterial communities associated with crab gills show transcriptomic shifts under different oxygen exposure conditions.
File handling & QC:
Merging FastQ files: cat
Read quality control: FastQC, MultiQC
Pre‑processing:
Adapter/quality trimming: Trim Galore!, fastp
Removal of genome contaminants: BBSplit, Kraken
Removal of rRNA: SortMeRNA
Alignment & quantification options:
STAR → Salmon
STAR → RSEM
HiSAT2
Post‑alignment processing:
Sorting and indexing: SAMtools
Duplicate marking: Picard MarkDuplicates
Transcript assembly/quantification: StringTie
Coverage files:
BEDTools, bedGraphToBigWig
Functional annotation:
eggNOG‑mapper
Quality control:
RSeQC
Qualimap
Differential expression & analysis:
DESeq2
Data analysis in R / Python