7.1. Salmon Software Package

1. Getting Started with Salmon

2. Building an index using the Cellecta DriverMap EXP Assay V3 configuration file (Download link):

salmon index -t DM_V3_human.fa.gz -i DM_V3_human_index

3. Quantifying the samples:

salmon quant -i DM_V3_human_index -l A \ -1 data/sample_R1.fastq.gz \ -2 data/sample_R2.fastq.gz \ -p 8 --validateMappings -o quants/sample_quant

4. After quantification:
   Once you have your quantification results, you can use them for downstream analysis with differential expression tools like swish, DESeq2, edgeR, limma, or sleuth. Using the tximport package, you can import Salmon’s transcript-level quantifications and optionally aggregate them to the gene level for gene-level differential expression analysis. You can read more about how to import Salmon’s results into DESeq2 by reading the tximport section of the excellent DESeq2 vignette. For instructions on importing for use with edgeR or limma, see the tximport vignette. For using Salmon with swish for transcript-level analysis, see the swish vignette. For preparing Salmon output for use with sleuth, see the wasabi package.

*Cellecta does not own the software package and is not responsible for maintaining them. Cellecta also provides custom data analysis services. Please email tech@cellecta.com for more information.