User: Albert

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Albert140
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140
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New User
Location:
Dublin, Ireland
Last seen:
2 years, 11 months ago
Joined:
3 years, 1 month ago
Email:
a*******@tcd.ie

Posts by Albert

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5
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Answer: A: Gene count table from STRINGTIE/BALLGOWN for WGCNA
... 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 ...
written 3.1 years ago by Albert140
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Comment: C: Gene names in Ballgown differential expression analysis
... 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 ...
written 3.1 years ago by Albert140
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Gene names in Ballgown differential expression analysis
... 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 ...
ballgown rna-seq written 3.1 years ago by Albert140 • updated 2.6 years ago by mcalleja80

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Student 3.1 years ago, asked a question with at least 3 up-votes. For Gene names in Ballgown differential expression analysis

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