Hi,
I ran successfully nf-core/rnaseq pipeline in the following way:
nextflow run nf-core/rnaseq
-profile singularity
-r 3.14.0
--input samplesheet.csv
--fasta /work/waterhouse_team/NB/LAB360/NbLab360.genome.fasta
--save_reference
--gff /work/waterhouse_team/NB/LAB360/NbLab360.v103.gff.gz
--outdir results
--aligner star_salmon
--trimmer fastp
--extra_fastp_args detect_adapter_for_pe,correction
-resume
How to use the output from the above pipeline to generate:
- A list of genes in our plant genome highly expressed in one tissue (four tissues in total), categorised by the tissue with the highest expression.
- For each gene above, the range of expression in TPM and the ratio between the highest and average expression in other tissues in a heat map.
Thank you in advance,