Hi everyone,
I'm currently working on a mRNA-seq which was performed by a private company. After obtaining the data, I'm filtering and trying to...
16 results in 0.0038 seconds.
-
About using or not FPKM threshold after DESeq2
-
Calculate Genotype Likelihood from raw data
I am working on amplicon data from an aploid genome (same length, already aligned with a miltiple alignment). Since I cannot generate a .bam file I've... -
demultiplexing multiple runs with and without samples same sample sheet
Hello all,
I'm going to demultiplex a run with a sample sheet in which there are entries and adapter sequences in the sheet with no corresponding... -
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... -
RNA-SEQ Quantification Pros/Cons using different features
I'm working with two replicates each for a two group pairwise comparison of single-end RNA Seq data derived from Illumina TruSeq v2, with fragments of... -
GAGE Pathview and gene counts
I am working on pathway analysis using GAGE and Pathview. I can determine up-regulated and down-regulated pathways and get corresponding heatmaps, but... -
error with htseq count and bed tool
hello every one,
as i am working on count based differential analysis and for that i am trying to use HTSEQ and bedtools
1. I am... -
Creating Count Table using BedTools2 (which "executables" do I add to PATH?)
As you may guess by the title, I am not very experienced with Linux. I have been trying to follow the advice on these websites:
https:... -
DESeq/EdgeR on counts of reads supporting variant
Is there precedent for and/or is it sensible to use DESeq or EdgeR to model counts of reads supporting variants in order to get significance?
...Last edited by brentp; 03-31-2014, 09:00 AM. -
glm edgeR issue
Hi everybody
I just performed a time series analysis on edgeR and I have a question.
This is my data frame for the condition and time:... -
Raw counts of 12 column bed file (against multiple BAM)
Hello Everyone,
I am sharing a perl script to get raw read counts from mulitple BAM files, for a given bed file. The script requires bedtools... -
DEXSeq gene level counts
Dear DEXSeq authors,
I have a question related to the following paragraph in the DEXSeq vignette:
I am wondering if this... -
more counts than total library size ?
Hello,
I have mRNASeq data displaying counts per splice variants of mRNA, and I was just wondering how it is possible that the total number of... -
HTSeq not working with Bowtie2 .SAM
Hi all,
I am having a weird problem with my Bowtie2 .SAM output for use with HTseq to count reads that correspond to genes in a .gff file.... -
Comparing densities of Chip-seq tag counts and plotting them
I have a matrix of Chip-seq results data like this for 26000 genes
LncRNA_ID LncRNA_Name Control_Raw_TagCount ICLIP_EZH2_Raw_TagCount...
