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Posts by Albert
... There's a python script called prepDE.py in the Stringtie manual, which gives you raw count tables from your stringtie output. Maybe that´s what you need. Check the manual to see how to run it. Manual: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual Script: https://ccb.jhu.edu/software ...
... Hi, you can get a table with all the information in your ballgown object (bg) , doing: full_table <- texpr(bg , 'all') The table will include: transcript id, chromosome, strand, start positon, end position, number of exons, length, gene id, gene name, and the FPKM values for each sample. Btw ...
... Hi there, I just performed an RNAseq experiment, for which I used HISAT2 for the alingment, Stringtie for the assembly and the R package Ballgown for the Differential Expression (DE) analysis (protocol published here: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html ). The defa ...
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