10. Read Quantification

Learning objectives:

  • Learn mapping and differential gene expression analysis of rna-seq data
  • Interpret rna-seq analysis results

10.2. Index the assembly:

salmon index --index nema --type quasi --transcripts Trinity.fasta

10.3. Run salmon on all the samples:

  • What are the flags used in the salmon command?
  • Read up on libtype, here.
for R1 in *R1*.qc.fq.gz
  sample=$(basename $R1 extract.qc.fq.gz)
  echo sample is $sample, R1 is $R1
  echo R2 is $R2
  salmon quant -i nema -p 2 -l IU -1 <(gunzip -c $R1) -2 <(gunzip -c $R2) -o ${sample}.quant

10.4. Take a look at quant output

head 0Hour_ATCACG_L002_R1_001.qc.fq.gz.quant/quant.sf

10.5. Look at all the mapping rates:

find . -name \salmon_quant.log -exec grep -H "Mapping rate" {} \;