I have stringtie reads count table (-B from Ballgown function) generated of which I used to perform deseq2 analysis. Please inform me how to use read count as input in deseq2 in galaxy. Tximport is not working for data.
the output generated when using the -B option in Stringtie cannot be used as input for DESeq2. The help section of the Strintie tool includes the instructions for using Stringtie + DESeq2:
DESeq2, edgeR and limma are three popular Bioconductor packages for analyzing differential expression, which take as input a matrix of read counts mapped to particular genomic features (e.g., genes). This read count information can be extracted directly from the files generated by StringTie (run with the -e parameter) by selecting DESeq2/edgeR/limma-voom under Output files for differential expression? above. This uses the StringTie helper script prepDE.py to convert the GTF output from StringTie into two tab-delimited (TSV) files, containing the count matrices for genes and transcripts, using the coverage values found in the output of StringTie -e.