Running OneStopRNAseq (OSR) with COUNT input

If users have a gene count-table, they can use this COUNT entry to perform quick DESeq2 and GSEA analysis with OSR. Below are the supported formats of count-table. Please click the example files to see the format. Besides the count-table, a meta-data file and a contrast file must also be provided. Please see the metadata format, and the contrast format for more information.

Description of count-table format

Three different formats of count table are supported

1. osrCount format

• Example file: osrCount.mm10.xlsx
• This is an xlsx file generated by OSR, typically stored as "DESeq2/COUNT.xlsx"
• The xlsx table header must be exactly: Gene Name Type SampleName1 SampleName2 etc.
• Support of this format allows quick re-analysis of gene-level analysis with updated meta-data/contrast info

2. featureCounts format

• Example file: featureCounts.mm10.txt
• A txt file generated by the featureCounts software
• The table header must be exactly: Geneid Chr Start End Strand Length SampleName1 SampleName2 etc.
• The separator of columns must be 'tab'
• Support of this format allows to run OSR with any featureCounts count-table obtained from collaborators, public database, etc.

3. cleanCount format

• Example file: cleanCount.mm10.xlsx
• An xlsx file that has gene-name or gene-id as the first column, and read counts in other columns
• The table header must be: Gene SampleName1 SampleName2 etc.
• Because no concatenated exon length (Gene length) is provided, TPM/FPKM normalization will not be performed, and DESeq2 normalized expression values will be used in the output tables instead
• Support of this format allows to run OSR with count-table generated with any software, so that users have more flexibility