Hi!
Im studying adipose and skeletal muscle tissue atm. As a quick sanity check of Cuffdiff results on isoforms, I want to look at well...
11 results in 0.0029 seconds.
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Isoform quantification, sanity check
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Cuffdiff results puzzling me. fpkm 350 vs 5.6 IS sig while 6 v 350 ISN'T ??
Hi all,
New to RNAseq analysis and trying to find DEGs with some PE seq data I've aligned using tophat. I just can't understand why cuffdiff... -
Cuffdiff q-values
I am having problem understanding the Cuffdiff q-values. I am using Cufdiff v.2.1.1 and I understand that in this version the lowest possible p-value... -
RSEM and cuffdiff
Hi,
I have just re-analysed my data to get TPM rather than FPKM values. I have done this using RSEM.
A google search has... -
Cuffdiff 0 tests with iGenomes?...
I'm trying to run a number of data sets with the most recent version of cuffdiff.
Previously with Cufflinks 2.02 I would provide cuffdiff... -
Cuffdiff calculations
Hi
Everyone
I have been trying to wrap my head around these problems and I am sorry if someone has posted these exact problems earlier:...Last edited by mparida85; 01-26-2014, 08:06 AM. -
Cuffdiff 2 progress reporting
Hi All,
I am running cuffdiff2 on 2 samples with 4 replicates each and a total of 160m reads (PE 80bp) for nearly 48 hours now, however I...Last edited by barkasn; 01-09-2014, 02:47 AM. -
Changes between Cufflinks/Cuffdiff version 2.0.2 and version 2.1.1
Hey All
I have analysed some RNA-Seq data for a mouse genome with both Cufflinks/Cuffdiff version 2.0 and 2.1 and get quite different results.... -
Cuffdiff problems
I'm running Cuffdiff v2.1.1 and am running into problems:
My script is:
...Code:cuffdiff -p 12 -o ./diff_out -b /ichec/work/nglif015b/nick/bowtie/bowtie-indexes/Laevis_7/Xl7.fasta
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EdgeR and GLM to look at significant ratios
Hello all,
I want to use a GLM in EdgeR on raw fragment counts generated from cuffdiff. I have 4 groups (A,B,C,D) with 4 biological replicates... -
multithreads -p option in cuffdiff
Hi guys,
I was wondering how cuffdiff handles multithreads, basically the -p option.
I'm right now at this step:
"Inspecting...
