Entering edit mode
9.4 years ago
f.muoghalu
•
0
Please, someone should help me on python command that will analyse calculate the Exon numbers, % scaffold identity, find the number of hits with high similarity in a row in the scaffold, check which scaffold is covered most, region in the scaffold, and % mapping. New in python but presently working on a project and I need a training on that.
I'm impressed! Most people would not make so many demands while putting forth such little effort.
State precisely what files you are working on. You used very broad terms like (exons, scaffolds, mapping, coverage etc)
Post what you have tried till now in python. Then people can modify your code if necessary. But no body will do it for you from scratch. Or you may search for existing tools. There are many tools available to deal with routine stuff.
Here you go, Learn Python in 10 min.
I'm going to read into "a python command" a little and wager that you're also new to programming. Before embarking on any research (assuming this isn't homework), I suggest that you get a solid grasp of python, BioPython and writing some code that performs basic calculations and manipulations of sequence data.
I'm also going to wager that you're new to bioinformatics, some of the things you're asking can be answered with sequence alignment tools such as BLAST. You should take time to familiarize yourself with the general features of your data; the methods used to obtain your data, the format your data is stored in, and the biological question you're investigating.
It sounds like you're trying to annotate some sort of sequence data based omic data. The general problem of annotating sequence data is common and many people have worked on it, look for resources on it. However, this problem is common between many different types of omics problems, each with their particular features and fine grained parts that can have serious impact on what you need to do and the quality of data you generate. I'm assuming exome, but I might be wrong.
You really have to have a very strong grasp of what the data captured, how it was captured, and what question(s) you're trying to investigate. There's nothing wrong with jumping into the deep end, but the first step is to get your head above water.
And on that note, you might want to have a look at this forum/thread