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Old 05-11-2015, 05:08 AM   #1
meghavarshney
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hello every one ,

i am a beginner for rna seq analysis, i would like to know that how to perform sample comparison (how to compare two biological replicates/varieties). and how to use fastq file for this purpose.

thanks
Megha Varshney
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Old 05-11-2015, 06:01 AM   #2
GenoMax
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Here is a general reference resource: http://en.wikibooks.org/wiki/Next_Ge..._%28NGS%29/RNA

Packages for doing differential expression analysis:
Tuxedo suite: http://www.nature.com/nprot/journal/....2012.016.html
edgeR: http://www.nature.com/nprot/journal/....2013.099.html
DESeq2: http://www.bioconductor.org/packages...doc/DESeq2.pdf
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Old 05-11-2015, 10:33 PM   #3
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thanks a lot sir ,
As may be I typed my question in a wrong way actually i would like to find out correlation between the two biological replicates at sequence level. can we do that.
One another thing how do we find out/ mark only PCR duplicates in my file.





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Old 05-11-2015, 10:49 PM   #4
meghavarshney
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thanks a lot sir ,
But i wuold like to find out correlation among two biological replicates at sequence level .. can we do that...





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Old 05-12-2015, 04:09 AM   #5
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Quote:
Originally Posted by meghavarshney View Post
thanks a lot sir ,
As may be I typed my question in a wrong way actually i would like to find out correlation between the two biological replicates at sequence level. can we do that.
One another thing how do we find out/ mark only PCR duplicates in my file.
Correlation is a statistical measure that isn't applicable to sequence. You could measure gene expression (counts) correlation between two samples.

Are you perhaps thinking of sequence similarity?

You can use dedupe.sh from BBMap or mark duplicates from Picard to mark duplicates. That said you should be careful about removing duplicates from RNAseq data. See http://seqanswers.com/forums/showthread.php?t=33597 and threads there in.
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