quant_sf2express_table is a DNAnexus applet that generates expression table files suitable for RNA-seq Expression Analysis (i.e BioJupies or iDEP) from a set of quant.sf files produced by Salmon.
Required Input Files
A Set of quant.sf Files – Select a set of files with naming convention sample_name_quant.sf. Where, you substitute sample_name with a unique sample name containing alpha-numeric characters and no spaces. You can obtain quant.sf files:
- Use GAU’s DNAnexus applet salmon_spg_wf, or
- Run Salmon to produce a set of quant.sf files, rename and upload to a DNAnexus project.
Output Files
- Expression HTML File – An output file that provides useful links, DNAnexus job information and instructions on submitting to BioJupies or iDEP which provide downstreamRNA-seq Expression Analysis.
- Raw Counts Table File – File containing table with unprocessed raw counts.
- TPM Counts Table File – File containing table TPM (transcripts per million reads) counts.
- Design Table File for iDEP – File used by iDEP containing table of sample names and conditions or treatments. The file can be opened in Excel or a text editor and customized.
For NCI Members
- Find out more about GAU’s DNAnexus Pilot Program.
- For NCI Members who want to use DNAnexus or develop you must get an account.
Developed by GAU
- Peter FitzGerald (email: fitzgepe@mail.nih.gov)
- Carl McIntosh (email: mcintoshc@mail.nih.gov)