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Genome Analysis Unit

About quant_sf2express_table …


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:

  1. Use GAU’s DNAnexus applet salmon_spg_wf, or
  2. 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


 

Developed by GAU