I have (very complex) artifact levels up to 95% in my total RNAseq data.
Some facts:
- NEB Ultra 2 Library prep
- 96 samples per plate,...
15 results in 0.0036 seconds.
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Total RNAseq library - artifact levels up to 95% with clear pattern on 96 well plate
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Working through CyVerse
Hi, I came across a review article on transcriptomic analysis suggesting that the post-sequencing analysis can be done through CyVerse (or initially known... -
Determining strandedness of .bam file (RSeQC)
Hello There,
I have recently begun analysis of some RNAseq data of Nicotiana benthamiana, under various pathogen type treatments. This... -
Genome Assembly vs Reference Genome for slicing around mutation location
Hello friends,
I have a bam file and corresponding vcf file from some source. I am trying to slice the DNA across its mutation... -
quantifying RNAseq reads for a genbank isoforme that is not in Reference Annotation
Hi, I'm trying to quantify different isoforms of a gene using RNAseq data. I have some bam files and I've tried assembling transcripts by cufflinks -G... -
Counting the total number of SNPs in a transcript
Hi,
I have RNAseq data that has been aligned to reference transcriptome and the aligned bam file is sorted and indexed.
... -
csScatter: Error in match(x, table, nomatch = 0L)
hello everyone,
i am getting this error in csScatter command.
...Code:> csScatter(genes(cuff)) Error in match(x, table,
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Adapter/primer trimming from RNAseq reads
Our lab had received RNAseq data from Illumina. I was able to do preliminary quality analysis using Fastqc app. Results are back however there seems to... -
RNAseq DE expresssion: remove reads from contamiinant species??
Hi all,
I'd like to pose you a question on RNAseq data analysis.
I did several RNAseq libraries on bivalve larvae (from hatchery... -
DESeq2 with nested design?
Hi all,
Is is possible to use a nested model in DESeq2 or EdgeR??
I have 3 treatments (evolution lines), but each treatment... -
Is The cancer genome atlas (TCGA) RNA-seq data strand specific?
Hi,
I have a simple question:
Is RNAseq data provided by TCGA project strand specific?
I am trying to search... -
TopGo, factor of 1 means
Hi,
I'm trying to do GO enrichment analysis using topgo, but i've encountered a problem, read below. what does factor w/ level 1 mean?... -
Cufflinks transcript.gtf single exon entries
Hi all,
How many exons have to covered in a transcript for Cufflinks to annotate that as a transcript? I noticed that some entries in the... -
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... -
any tools to test if my RNAseq data is enough?
Hi,
I am new to the field of RNA sequencing.I have read a lot of message about how many reads is enough for RNAseq,but it seems that there is...
