SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
quality control from fastq to vcf dongshenglulv Bioinformatics 3 11-05-2014 03:08 PM
Quality control of genomic resequencing data from a HiSeq gavin.oliver Genomic Resequencing 2 06-30-2013 02:48 AM
Webinar on Quality Control of NGS Data - FREE Strand SI Events / Conferences 0 09-09-2011 07:33 PM
TileQC: a system for tile-based quality control of Solexa data ScottC Illumina/Solexa 0 06-03-2008 05:54 PM
PubMed: TileQC: a system for tile-based quality control of Solexa data. Newsbot! Literature Watch 0 05-30-2008 09:21 AM

Reply
 
Thread Tools
Old 06-02-2017, 08:13 AM   #361
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,550
Default

@Phil: Is a better fix coming along for this? That kind of seems like a hacky solution.
GenoMax is online now   Reply With Quote
Old 06-03-2017, 12:25 AM   #362
ewels
Phil Ewels
 
Location: SciLifeLab, Stockholm, Sweden

Join Date: Mar 2011
Posts: 31
Default

Quote:
Originally Posted by GenoMax View Post
@Phil: Is a better fix coming along for this? That kind of seems like a hacky solution.
No idea You'll have to ask Simon about that..
ewels is offline   Reply With Quote
Old 08-30-2017, 12:29 PM   #363
fnn4
Junior Member
 
Location: USA

Join Date: Jul 2014
Posts: 8
Default

Hello,

Does any one know where I can find average Q score on miseq raw reads fastQC report? I know fastQC gives per sequence Q scores. But it doesn't tell the average Q scores of the raw reads though. Thank you very much in advance.
fnn4 is offline   Reply With Quote
Old 08-30-2017, 12:49 PM   #364
ewels
Phil Ewels
 
Location: SciLifeLab, Stockholm, Sweden

Join Date: Mar 2011
Posts: 31
Default

Hi @fnn4,

Do you mean a single mean quality score for the entire FastQ file? The Per Sequence Quality Scores plot shows the distribution of average Q scores across all reads in the file. I don't think that FastQC reports an average for the entire file, but it should be simple enough to do using the raw data reported in fastqc_data.txt - just sum the (Q score * read count) from the per-sequence section and divide by the sum of the read count.

What's your reason for wanting this statistic, out of interest?

Phil
ewels is offline   Reply With Quote
Old 08-31-2017, 07:30 AM   #365
fnn4
Junior Member
 
Location: USA

Join Date: Jul 2014
Posts: 8
Default

Hi Phil,

Thank you for your reply. Yes, that is what I was asking for. When we submit samples, we have to pass a certain threshold for average Q score.
Quote:
Originally Posted by ewels View Post
Hi @fnn4,

Do you mean a single mean quality score for the entire FastQ file? The Per Sequence Quality Scores plot shows the distribution of average Q scores across all reads in the file. I don't think that FastQC reports an average for the entire file, but it should be simple enough to do using the raw data reported in fastqc_data.txt - just sum the (Q score * read count) from the per-sequence section and divide by the sum of the read count.

What's your reason for wanting this statistic, out of interest?

Phil
fnn4 is offline   Reply With Quote
Reply

Tags
fastq, quality, report

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO