NGS data analysis

I have a question for deg analysis tools
written 3.7 years ago by likeabboo 1

Hi. I'm going to do DEG analysis with tmp data that has already been normalized. I want to use a total of four tools; DESeq2, …
How to retain genomic coordinates (chr, start, end, strand) of genes when going from StringTie to B…
written 4.3 years ago by akainth 3

After re-estimating my transcripts using stringtiemerge with -eB option, I want to do differential expression analysis at the gene level. For that, I tried Ballgown …
Differential expression using Ballgown
written 4.7 years ago by Heeba 0

I am running Differential expression analysis on stringtie output using Ballgown. My pData is : head(phen_data_Early) ![phen_data_Early][1] I extracted fpkm values using texpr, and have …
Error in prepDE.py after StringTie quantification
written 6.0 years ago by Lorenzo 1

Hello, I am doing RNA-seq analysis, using the pipeline suggested here ([http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq][1]). I utilized StringTie to map my reads, to assemble transcripts and to estimate …
Which pipeline is the best for differentinal gene expression analysis (edgeR, DESEQ2 or HISAT2 - st…
written 6.1 years ago by sunnykevin97 100

HI, I may asking a naive question, to clarify myself. Which RNA_seq pipeline considered to be the best for model and non-model organisms ? I …
Subset Function in Ballgown
written 7.0 years ago by Morgan S. 9

Hello, I am using the HISAT, Stringtie, and Ballgown pipeline to do transcriptome expression analysis. So far I went through these steps. bg=ballgown(dataDir=data_directory, samplePattern='1and2', meas='all') …
getting the test results of multiple transcripts; even though, I am using gene-level analysis
written 7.7 years ago by Fawzi Yassine 2

Hi, I am using RNAseq analysis to find genes differentially expressed between 2 conditions. I am using StringTie for transcript assembly and quantification. In ballgown …
Proper design for DESeq2 and other RNAseq general questions
written 8.2 years ago by Stef 0

Hello, I am new to the RNAseq. I sequenced 20 libraries from Eucalyptus. They are all different tissues: early flower, late flower pollinated, late flower …
Ballgown finds few DE genes compared to DESeq
written 8.4 years ago by corend 7

I have RNA-seq data with 2 conditions and 3 replicates per conditions. I ran the [New Tuxedo pipeline][1] and also created some [read count tables][2] …
Stringtie -> ballgown: What normalization should be done on FPKM values?
written 10.7 years ago by njbernstein 4

Hi all, I used stringtie to quantify an rna experiment and then loaded that data into ballgown. The standard unit used by ballgown is FPKM, …