Tweet
de novo assembling sequences to do go or pathway analysis
hi! here is my problem: i have some sequence assembled by trinity ,with raw data and downstream Trinity scripts ,a list of Differencial Expression seqs were collected. i wanna do GO and Kegg analysis with those sequences and i have no idea on how to do it cause there is no reference genome .so can anyone give me some advice or recommand some software to do this? thanks!
-
-
De novo sequence analyses
Hi! I am using Blast2GO (http://blast2go.com/b2ghome) for my de novo analyses. You just have to upload your sequences in a fasta format and first blast them against the online database before getting any GO terms for your sequences. You can also get the information in which pathways your annotated genes are represented through KEGG. I hope that helps!! I do not know yet about any other programme, which can do GO and KEGG for de novo analyses.
Good luck!
-
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
-
I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
Comment