[BioC] Hello

[Wei Shi]

Dear jayakumar,

The Rsubread package seems to be able to do most of your tasks. Have a look at its users guide for details about the read alignments it performs:

library(Rsubread)
RsubreadUsersGuide()

It has two functions to check the quality of sequencing data:

?qualityScores
?atgcContent

It can also detect SNPs:

?callSNPs

Its users guide also includes a case study for analyzing RNA-seq data, including read alignment, read summarization and differential expression analysis.

Best wishes,
Wei

On Sep 26, 2013, at 8:45 AM, jayakumar sivalingam wrote:

> Hello,
> Please let me know about the bioconductor packages to be used for the
> following things:
> 
> 
>   1. Quality check of the whole genome raw data
>   2. Alignment
>   3. SNP identification
>   4. Annotation
> 
> Also, please let me know how I can be able to practice the above things
> with the example data and the system requirements for the same.
> 
> Thanks & regards,
> Jai
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:6}}