Dear Arash,
there is a RNA-seqlopedia and simple Guide for RNA-seq that area very good refrences to begin (maybe you are already familiar with them).
And you can search for "5.2.4 Filtering/Normalizing Reads by k-mer Coverage" and "Table 5.1 Read Processing Software " that compares some trimmer software in the first one.
In any countries there are good and not-good persons and it does not play very important role in your research, I am also planning to setting up a Bioinformatic-helper website in Farsi, Insha Allah!
~Best
hi Farbod,how can I have your email?I think you are an Iranian experience student, my email is elhamdallalbashi@gmail.com
Arash, Salam! Man pederam Irani ast! Khosh amadid!
It seems as though you might be a beginner. Here is a link to a RNA-seq pipeline i use that has some quality control steps. If you want the imageplot.r function, I can send it to you.
Hi Arash,
By the way, there is a book in Persian and it may be help you about some NGS concepts (of courrse there is no R in it )
The input into R is a counts table, so what you need to do is align your reads and get a counts table. If your computational situation allows (RAM > 30gb), I'd recommend using star RNA-seq aligner.
Log in to answer this question.
Hi, Arash Jan,
please search for Quality reports for FASTQ files in systemPipeR.
and FASTQ quality report
~Best
Hi Farbod JAN,
What's the input data format?