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... -
FINAL CALL: RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
Exciting News from ecSeq Bioinformatics GmbH!
We're thrilled to announce the return of our RNA-Seq Data Analysis Workshop in March!
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cufflinks does not understand strands?
Dear All,
I used STAR to map paired-end reads onto the reference genome:
...Code:~/apps/STAR/bin/Linux_x86_64/STAR --runMode
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Can Cufflinks report chimeric transcripts/fusions?
I understand that Cufflinks can report FPKM on novel transcripts (different isoforms) if using proper parameters, but I wonder whether cufflinks is able... -
Cuffset number of genes too high
Hi,
So I'm implementing a pretty standard tuxedo pipeline on paired-end mouse data. I went along as follows.
Using the... -
Confidence of cufflinks denovo predicted eons
I'm using cufflinks denovo and cuffcompare to find un-annotated exons (in mouse as well as other genomes). When viewing the exons predicted by this pipeline... -
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... -
Any advanced CummeRbund tutorials out there?
Any advanced CummeRbund tutorials out there? I've only found tutorials that cover the basics in the manual. I'm looking for something more detailed... -
Cufflinks---no response after run
Hi all,
I am suffering a very strange problem in running Cufflinks and hope you can help to solve this:
1. I had run Cufflinks... -
2 treatments and 1 control, a three way normalization for cufflink output
I have 2 treatment samples -A and B and they both need to normalized to control sample before I compare between A and B itself. How do I do this with... -
Tuxedo pipeline: cufflinks with -G option vs cuffdiff with reference
Dear all,
I have been analysing RNAseq experiments using the default tuxedo pipeline for about a year, i.e., TopHat2 + cufflinks + cuffmerge... -
cufflinks: input alignment from hisat2
Hi all,
I read on Cufflinks man page that input bam file must be sorted this way:
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted... -
Brainstorming: Error sources for Cuffquant failure: Map Mass: 0.00
Hello folks,
I have an issue with Cuffquant v2.2.1, which fails to quantify the expression (create .cxb files) of the current RNA-seq I am...Last edited by Thias; 07-22-2016, 02:33 AM.
