Mpileup for RNA-Editing. RNA-Seq analysis. PacBio RNA-seq protocol. From RNA-seq reads/alignments data to GFF Files. Normalizing count data in RNA-seq. Hello, Suppose I have RNA-seq data for 1) control, say, T0 2) treatment after 4 hours T4 3) treatment after 8 hours T8 and I would like to find out those genes that are differentially expressed between each of these pairs (where T0 vs T4 and T0 vs T8 are most informative/essential to the experimenter).
I perform normalization using edgeR TMM method. However, the way I have been doing it is to normalize count data for each pair (A). That is, for T0 vs T4, I obtain the counts and then perform the TMM normalization and then obtain the candidate genes and then for T0 vs T8, once again do normalization between these two count data and obtain DE genes and so on... However I am beginning to wonder if this is the way to go or to perform only one normalization by having counts from all genes from all time points altogether (B). I am not able to convince myself of a good reason to choose between either. Thank you. RNA-Seq Paired end analysis.
Shared Read Analysis Between Two Small RNA Libraries. What databases are available for RNA-seq datasets? Gene count data filteration - BioStar. 2.4 years ago by Barcelona, Spain.
Hi, I am generally not at ease with filtering, moreover with RNA-Seq data. This makes quite some sense for microarray data since non-expressed genes also had a low intensity signal (even though there is no gold standard methods of filtering). For RNA-Seq, there is no such drawback and the presence of at least one unambiguously mapped read on a gene should normally reflect an evidence of transcription. My opinion would rather be to control if the results of your analyses are not biased by such genes, dividing your initial gene set in several bins of expression.
. • link modified 2.4 years ago • written 2.4 years ago by Philippe • 1.6k. How to find stranded RNA-Seq experiments data. MiRNA target prediction. RNA extraction for frozen tissue sample. MiRNA target prediction. Perturbation of a RNA secondary structure. 2D RNA structure for proteins. Hi everyone I have two datasets of proteins, Secreted and cytoplasmic.Each set includes at least 10 genes.
I get their RNA cods and I want to look at their structures to figure out whether there are any similarity shape or pattern in each sets or maybe what is the major difference between them !! I did the following: I'm interesting only in first 12 codons, so I cut the sequences to 12 letters only.I used MATLAB to get their DNA sequences and then their RNA sequences from its DNA cods. I have plotted their 2D structure by MATLAB using following cods: seq = rna(1:36); ss = rnafold(seq); rnaplot(ss, 'sequence', seq, 'format', 'diagram'); the results was very tricky.
I'm thinking now if there is any statical analysis that shows some quantitative measurement? Is my way of thinking wrong ? I did local alignment between seq in each class, and it shows some similarities region between the beginning of seq. and middle seq. as well. Any suggestion to reach my goal? Nana. Poly A sequences in small RNA. Q-PCR for RNA-Seq Data. Retrieving sequence from noncoding RNA. Correct draft paper on siRNA and miRNA. NM accession numbers to get mrna seq.
Duplicated reads in RNA-Seq Experiment. 2.4 years ago by How many reads (percentage) would you expect to be exactly equal?
And to what extent? I just came across an experiment where out from 100 x 10^6 reads, just 60 x 10^6 reads are unique. In my case, it is rna-seq of a murine adipocyte cell line. Illumina HiSeq, paired end reads, read length = 100. Actually I do think it is due to some error in the library preparation. I just wonder what to do with such data. Moreover, one could reduce the computational cost of the mapping dramatically if one deals with such data and restrict the data to just unique reads. How do we know if miRNA is in stem. Small RNA (miRNA) mapping. Can SOAP2 be used for RNA-seq analysis. Poly(A) tail from RNA-Seq?