# Introduction of OSR from COUNT input If users have a gene count-table, they can use this to perform quick DESeq2, GSEA analysis and visualizaiton of RNASeq data. # Description of count-table format Three different formats of count table are supported 1. osrCount format - e.g. example_data/counts/featureCounts.mm10.txt - an xlsx file generated by OneStopRNASeq(OSR) as DESeq2/COUNTX.xlsx - table header must be exactly: Gene Name Type SampleName1 SampleName2 etc. - designed to re-run gene-level analysis with updated meta-data/contrast info quickly 2. featureCounts format - e.g. example_data/counts/featureCounts.mm10.txt - a txt file generate by featureCounts software - table header must be exactly: Geneid Chr Start End Strand Length SampleName1 SampleName2 etc. - the seperator of columns must be 'tab' - designed to run OSR analysis with any featureCounts count-table obtained from collaborators, public database, etc. 3. cleanCount format - e.g. example_data/counts/cleanCount.mm10.xlsx - an xlsx file that has gene-name or gene-id as the first column, and read counts in other columns - 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 - designed to run OSR analysis with count-table generated with any software, so that users have more flexibility # Description of meta-data file: - e.g. example_data/meta/meta.xlsx - an xlsx file that describes each sample - must have the following header: SAMPLE_LABEL GROUP_LABEL BATCH - sample labels in meta-data and count-table must be exactly the same, any typo, or missing/additional sample labels in meta-data will stop the analysis # Description of contrast file: - e.g. example_data/meta/contrast.de.xlsx - an xlsx file that describes the comparison/contrast of groups that is of research interest - all GROUPS listed must be included in the GROUP_LABEL column of meta-data file, typos will stop the analysis or give wrong results - if you are interested in combining multiple GROUPS in the comparison, please use semicolon to seperate them - results will be the comparison of row2-GROUP vs row3-GROUP