Dear All,
Please inform,
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.
Thanks
Hi @KMS_KMS,
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.
Regards
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