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• Are Reads Of 36Nt In Length Long Enough To Accutatly Map On Splicing Junctions?
  Hi All, I have a very basic question. I have RNA-seq datasets of several cell types and want to ...
• Should I Use Igenomes Verson Of A Reference Gtf For Tophat?
  Dear All, I am analysing RNA-seq datasets for differential splicing events between cell types. T...
• How To Find The Alternatively Spliced Segment Of Genes In Cuffdiff Output
  Dear All, I have run programs from Tophat to Cuffdiff of Galaxy to look for the difference in al...
• How Much Can I Trimm My Reads
  Dear All, I am analysing RNA-seq datasets for the differential splicing events between cell type...
• What Is The Minimum Quality Should I Set For Filter Fastq?
  Dear All, I am analysing RNA-seq datasets for differential splicing events between cell types. ...
• cufflink only assembles 1 transcript for gene of interest when tophat splice junctions suggest different alternative splicings
  Hello Friends I am currently doing RNA-seq hoping to find new transcript (we found with our qPC...
• Profiling a Small Number of Single Cells
  Hi, Hopefully I have posted this in the correct place. I have recently started in a lab and hav...
• Single cell RNA seq data set alignment
  Hello, I have a single cell RNA seq data (600 cells) and I would like to see the possibility to...
• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• RNA-star: splice junction
  Hello, I am new to RNA-seq data. I am using the built-in index and using the reference genome wi...
• RNA seq analysis
  i have done RNA seq on S2 Drosophila cells and want to check differential expression. I have my d...
• Rna-Seq Cds, Splicing And Tss Fails
  Hi all, So I am using cuffdiff to find significant differences between two samples (no replicat...
• how to extracts mRNA sequences with different Poly(A)tail lengths from RNA seq data
  I am trying to compare poly(A) tail length of mRNAs in cells with different condition both at glo...
• How Much Fpkm Can Be Take Into Consideration When Compare Gene Expression
  Dear All, I am comparing the gene expression between two cell types by examining the Cufflink ou...
• Minimum Length Of Read Segments
  Dear All, I am going to run Tophat with RNA-seq dataset to observe alternative splicing events. ...
• Should I "Use Raw Junction" And "Only Look For Supplied Junctions"
  Dear All, I have two more questions about settings for Tophat. My aim is to look for the deffer...
• Please Help To Understand The Square Root Of Jensen-Shannon Divergence
  Dear All, I am looking for the differential splicing events between cell types. However the Cuff...
• Tophat
  Dear all, Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using ...
• Variation in alternative splicing across plant tissues
  Dear all, I am trying to identify AS events from different tissues (5 tissues). and I did that u...
• small RNA seq using Illumina iSeq100
  Hi there, I just made small RNA seq libraries using the Illumina TruSeq Samll RNA LIbrary kit fro...
• Single Cell RNA-Seq Pipeline?
  If I want to analyze single cell RNA-Seq data in Galaxy, what is the best pipeline to use? I've b...
• Where is "Tophat for illumina Find splice junctions"?
  Dear Sir/Madam: This is Bob. I am interested in the course of RNA-seq-analysis-mapping. The demo...