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Old 12-29-2014, 10:36 PM   #1
nareshmvr
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Default Preprocessing for good quality reports of FastQC for RNA-Seq

Dear all,

I am newbie to RNA-Seq data analysis(Illumina) , i have done quality check using FASTQC for the RNA-Seq data and now as per the manual for evaluating the FASTQC reports, i got good quality for all the sequences except "sequence duplicates" and "per base sequence content" where in the manual of evaluating the reports they mentioned they can be ignored for RNA-Seq data.

In some forums i found irrespective of FASTQc reports , its a good idea to preprocess the data. so am confused how to preprocess the data for good quality reports of FASTQC , please suggest me in this about the tools and parameters for preprocessing good quality data , here am sending of my sample in the attachment. please suggest me if am wrong in this.

Last edited by nareshmvr; 12-30-2014 at 12:08 AM. Reason: image not sent
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Old 12-29-2014, 11:57 PM   #2
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is my question wrong , please let me know if am wrong
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Old 12-30-2014, 03:26 AM   #3
GenoMax
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"pre-processing" here is referring to use of a trimming program to scan your samples for adapter contamination? That is always a good idea irrespective of what the initial QC report says. You are not going to lose any information/make things worse by running BBDuk or Trimmomatic on your samples.
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Old 12-30-2014, 02:34 PM   #4
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thank you max ,

i have bit experience in using prinseq , am using params -ns_max 0 and derep 14 to remove exact duplicates and ns , please suggest me in this
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Old 12-30-2014, 04:35 PM   #5
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Take a look at this thread before you decide what to do with the duplicates: http://seqanswers.com/forums/showthread.php?t=33597
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Old 12-30-2014, 10:32 PM   #6
nareshmvr
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sorry i think i made a wrong approach about my confusion in the pre-processing step, how to assess the parameters in pre-processing step for the FASTQC report of a RNA-Seq data .
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Old 01-01-2015, 05:36 AM   #7
GenoMax
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Quote:
Originally Posted by nareshmvr View Post
sorry i think i made a wrong approach about my confusion in the pre-processing step, how to assess the parameters in pre-processing step for the FASTQC report of a RNA-Seq data .
Based on your original post it sounds like your data may already be of good quality and may not need additional processing.
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