4
votes
2answers
56 views

GO terms for non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have ...
4
votes
1answer
44 views

RNA-seq Data on domestic animal with different environment

I want to find the RNAseq data available on domestic animals in different environments. If microarray data is available, it would be more useful. If you know I would appreciate to inform me.
2
votes
1answer
353 views

RNA-seq analysis - q-values in cuffdiff

I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change ...
2
votes
0answers
94 views

Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have ...
1
vote
1answer
523 views

Problems with analysis of small RNAseq data - Adapter trimming

I have always faced a problem while analyzing small RNAseq data, at the step of adapter trimming. Overview of small RNAseq (Illumina) RNA is size fractionated using columns or PAGE 3' and 5' ...
2
votes
0answers
133 views

Too few transcripts from transcriptome assembler Oases

I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks. Here is my running command: ...
7
votes
1answer
4k views

Difference between strand-specific and not strand-specific RNA-seq data

I would like to ask the difference between strand-specific and not strand-specific dataset. As far as I know, strand-specific data means that we know which strand the transcript is from. I do not ...