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-   -   RNA seq analysis in R/BioConductor (http://seqanswers.com/forums/showthread.php?t=60508)

fing 06-18-2015 02:09 AM

RNA seq analysis in R/BioConductor
 
Hello,

I am completely new to RNA seq data and have just received my first set of data. I research analysis options online in preparation and favoured the R/BioC setup due to my extensive previous experience in R more generally.

The pipeline I have found instruction for is fairly simple:
1. Alignment of reads to reference using QuasR
2. Count reads
3. Normalisation
4. Identify differentially expressed genes
... with upstream analysis suggestions.

My query is with the initial stages. There is not a separate stage of QC/cleaning, but my understanding of QuasR is that it produces a QC report with quality scores for each sample, and also a FastQ report with information on sample quality, proportion of bases, read lengths.

Is this what is needed for QC before moving onto the next stage in the pipeline, or am I missing something? If I am missing something, any advice on where to look to complete the QC - especially in R/BioC! - would be very gratefully received.

Thanks in advance to all!

westerman 06-19-2015 09:43 AM

In general when mapping sequences to a known references (either genomic or transcriptome) there is no need for cleaning of the reads. They will map leaving the poor quality bases behind.

For de-novo work cleaning does need to be done.


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