Hello everyone,
I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave...
28 results in 0.0031 seconds.
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splitting Tophat2 bam files in separate samples
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HISAT2 not reporting all splice sites?
I'm using HISAT2 (version 2.0.5) to try and find novel splice sites. Going through the SAM file it produces suggests that there are a number of alignments... -
SplicingCompass: error in processing CoverageBed files
Hey,
I want to do differential splicing analysis using SplicingCompass (http://www.leibniz-hki.de/files/cont.../oeffentliche_... -
Junctions.bed file in hisat2?
Hi,
I was wondering if there is a way I can generate junctions.bed file from hisat2 just like the one in tophat.
Hisat2 documentation... -
MISO annotations
I have downloaded MISO annotation files for hg19, applied the MISo algorithm for a BAM aligned to hg19, and noticed that some annotations' event name...Last edited by rlv; 02-02-2017, 12:20 PM. -
MISO: Best-guessing insert size and stddev versus running single-ended for PE data
I am conducting a miso analysis for a single gene on a large number of Paired End RNAseq bams that is spread out on several external HDs (twenty 4tb drives).... -
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 ... -
SpliceR- Splice Graphs and Alternative Splicing
Hi everyone,
Has anyone used spliceR for RNA-seq in Arabidopsis?.
If yes, then kindly tell me how to assign a browser other than... -
My Sanger sequencing results do not fit to RNA seq
Hi everyone,
I am having troubles with proofing the results I obtained in Sanger sequencing by other methods.
At the beginning... -
Alternative splicing versus incomplete splicing?
In cDNA generated from poly-A reverse transcription of RNA, is it possible that PCR will detect incompletely spliced mRNA? How does one differentiate... -
Splicing using cuffdiff
Dear colleagues,
Thanks for this source of information that is Seqanswers, and thanks to many experts that share their knowledge and time... -
Validation of Splicing Results from cufflinks-cuffdiff pipeline
Hi
I am shortlisting my candidates for validation using qPCR/RTPCR of my results from two different splicing pipelines(DEXSeq & Cufflinks/Cuffdiff).... -
Quantify ration of spliced to unspliced reads
Hello,
I am interested in measuring the ratio of spliced to un-spliced genes in an RNA-seq experiment. Is there a method/technique/tool that can... -
Extracting statistically significant differentially expressed exons from DEXseq resu
Hi
I am trying to extract some data from my DEXseq results. I was able to get the final HTML report for my analysis. However, I was wondering...
