QC of RNA seq reads in R

Question

[Arash]

Hi colleagues, Regarding QC of RNA-Seq , what's the package for RNA seq QC in Rstudio?

[Farbod]

Hi, Arash Jan,

please search for Quality reports for FASTQ files in systemPipeR.

and FASTQ quality report

~Best

[Arash]

Hi Farbod JAN,

What's the input data format?

Answer 1

[Farbod]

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

[elhamdallalbashi]

hi Farbod,how can I have your email?I think you are an Iranian experience student, my email is [e-mail]

Answer 2

[datascientist28]

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.

https://rpubs.com/achitsaz/97976

[Arash]

Salam, Mamnoonam..Omidvaram Ok bashid.Amri?

Thanks so much for your help ,We have some knowledge share problem in Iran.As the NGS in Iran is new and hot, a few people (just one or 2 persons) are ready to help.

[Farbod]

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 )

here is the link

[Arash]

Hi again, I have the data in fq format. In "R", what's the file format input?

[datascientist28]

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.