Quality Control, Read Mapping, Visualization and Downstream Analyses
When? March 24 - 27, 2025...
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In-Person Workshop: Bulk RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)
RNA-Seq Data Analysis Workshop
Quality Control, Read Mapping, Visualization and Downstream Analyses
When? March 24 - 27, 2025... -
Comparing MiSeq output from different runs
Hi, I have about 4 different MiSeq runs i have data for. I have pipelined the fastq files through bowtie-samtools-cuffdiff to compare cDNA libraries of... -
KEGG with pathview using CuffDiff data
Hey everybody,
I am a newbie in coding in Bioinformatic and I have a question.
Using a HPC I perform a quality control and... -
Analysing only exons from ONE gene using RNAseq
I know that DEXseq and/or Cuffdiff etc. may be used of exon-levels analyses.
However, I am only interested in ONE gene, because a novel...Last edited by sindrle; 03-11-2017, 08:01 AM. -
How can I select my Chip-seq genes (targets) in my Rna-seq data?
Hi, I want to select my target genes found in my ChIP-seq data (Genes Names by HOMER) within my Cuffdiff output list of differentially expressed genes... -
Cuffdiff - Error: number of labels must match number of conditions
Hi,
when I tried running cuffdiff on two files (output from STAR) it would give me the XS label missing error, then I changed my command... -
Cuffdiff not generating the fpkm values
Hello All,
I am trying to generate a python pipeline to analyze RNASeq data. I am able to build an index of the genome, align the fastq... -
Help with sorting sam files in python!
Hello All!
I am new to coding. I have written a python script to analyze a bunch of fastq files from RNASeq analysis. I am using the subprocess... -
cuff diff error
The cuffData.DB file generated does not have any data. I guess I need this in order to proceed with cummeRbund.
The other files produced... -
spliceR: problems in detecting NMD sensitivity from RNA-seq data
Hello everyone,
I want to detect the NMD sensitivity from RNA-seq data of my Arabidopsis mutants. I read that spliceR can be used for this.... -
NOTEST everywhere with cuffdiff
Hello, I am running the following pipeline:
tophat -p 4 -G genes.gtf -o sample1TopHat genome sample1R1.fastq sample1R2.fastq ... -
how does cuffdiff calculate replicate FPKM values?
Hi,
I have two conditions, 5 replicates for each. After running cuffdiff I noticed the FPKM values in gene_exp.diff for one condition do... -
Cuffdiff confidence intervals - relative quantitation
Hi all,
I have not found any answers to this kind of question anywhere so I have to ask.
I've done RNA-seq and analyzed it in tophat/cuffdiff... -
Reads Mapped but 0 FPKM for Every Gene
Hi all,
I'm using Tophat 2.1.0 and Cufflinks 2.2.1 to analyze mouse RNA sequencing. I used Tophat to align the reads, and this step appeared... -
shiny_cuffdiff: On-the-fly interrogation and plotting of gene expression results
Hi all. I'd like to introduce the community to shiny_cuffdiff
http://nzgl.github.io/shiny_cuffdiff/
Put simply, this code...
