Rna Seq To Protein Seq Conversion

Question

[inambioinfo]

Hi,Am new here to the group and probably my first question as a Newbie to RNA seq data analysis. I have three question to ask here.

1. May i get any workflow to process my FASTQ file and get expression analysis (this is basic question I know but am not aware which tool i have to use and there are many for each and I want to know what are all the steps involve in Raw Data analysis like preprocessing or Quality Control check.

2. I could like to know how i can convert this RNA seq to Protein Seq is there any tool already available or we need to programme by ourself(if Yes, Then please let me know what's the science behind these conversion and how does it work. this will help me to code my program by myself).

3. How many junction protein is there in Human( all type of junction like exon junction or alternative junction analysis protein etc) I will be more happy if i get any reference paper which illustrate the number of Junction.

Wish to hear from you and Thanks in advance.

Answer 1

[Devon Ryan]

1. Have a look at galaxy as there may be prepackaged workflows that you can learn from. The general steps would be (1) adapter/quality trimming (trimmomatic is a popular choice) (2) QC with fastQC (3) alignment (tophat2 or STAR are common choices) and finally (4) counting reads per gene (htseq-count or featureCounts are the common choices).

2. This sort of depends one what you actually mean by "protein-seq". Normally, that would refer to something completely different and there's no conceivable conversion because it's simply a different type of experiment. Perhaps you mean "go from RNA to protein sequence", in which case just look up what a codon is (you can just do this in R or biopython or bioperl without much fuss).

3. I've never counted, but most genes are spliced. If you actually want to count by proteins rather than by genes then the common guesstimate is ~100k (there would then be many more exon-exon junctions).