SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Threshold quality score to determine the quality read of ILLUMINA reads problem edge Illumina/Solexa 35 11-02-2015 10:31 AM
Quality Score: FastQC vs Illumina ericguo Illumina/Solexa 8 10-22-2015 04:08 AM
Why is the base quality score so different between FastQC and FastX? TheStudent Bioinformatics 7 06-08-2012 08:44 AM
Threshold quality score to determine the quality read of ILLUMINA reads problem edge General 1 09-13-2010 02:22 PM
Fastq quliaty score and MAQ output quality score baohua100 Bioinformatics 1 02-19-2009 09:21 AM

Reply
 
Thread Tools
Old 10-04-2012, 12:10 PM   #1
newBioinfo
Member
 
Location: US

Join Date: Mar 2012
Posts: 36
Default Fastqc:how to get a quality score for individual read

Hi Everyone,
I have a 77 million reads and I need to know the quality score of each read so that I can filter the data based on the quality score. I used Fastqc and it gives me the graph of quality score of each read. But I need to know in a file how much is the quality score of each read. Is there any way I can get that.
Please help!!!
newBioinfo is offline   Reply With Quote
Old 10-04-2012, 12:21 PM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Quote:
Originally Posted by newBioinfo View Post
Hi Everyone,
I have a 77 million reads and I need to know the quality score of each read so that I can filter the data based on the quality score. I used Fastqc and it gives me the graph of quality score of each read. But I need to know in a file how much is the quality score of each read. Is there any way I can get that.
Please help!!!
I'm pretty sure there is no single value for that. Individual bases have quality scores, a read can have a mapping score, which is entirely dependent on the reference you give it, but I don't know of a single quality score for an Illumina read. You could get all the reads with 80% of the bases >Q30, or trim all the 3' bases with <Q5, or somethinig like that.
swbarnes2 is offline   Reply With Quote
Old 10-04-2012, 12:50 PM   #3
mnkyboy
Member
 
Location: Seattle, WA

Join Date: Mar 2009
Posts: 87
Default

You can use fastx to filter based on your desired quality score.
mnkyboy is offline   Reply With Quote
Old 10-08-2012, 03:03 PM   #4
billstevens
Senior Member
 
Location: Baltimore

Join Date: Mar 2012
Posts: 120
Default

Sorry, very basic, very quick question. I have very good 100bp PE data (Illumina Phred Scores ~33). That usually holds all the way through from base 1 to 100. However, there are some reads that are low quality, and sometimes, at the 3' end of some reads, the quality dips very low, but not often.

Since the quality doesn't dip often at any end, I think trimming is a bad idea, but I still should filter reads based on a certain quality score, right??
billstevens is offline   Reply With Quote
Old 10-09-2012, 07:56 AM   #5
billstevens
Senior Member
 
Location: Baltimore

Join Date: Mar 2012
Posts: 120
Default

bump? Sorry for the simple question. I wasn't filtering, but I went to a workshop that said you should always filter/trim, and I just wanted to have one more confirmation.
billstevens is offline   Reply With Quote
Old 10-09-2012, 02:48 PM   #6
billstevens
Senior Member
 
Location: Baltimore

Join Date: Mar 2012
Posts: 120
Default

Also, sorry, does anyone know how to filter more than one file at a time with Fastq?
billstevens is offline   Reply With Quote
Old 10-09-2012, 03:18 PM   #7
fubar
Crusty old bioinformatician
 
Location: Melbourne, Australia

Join Date: Oct 2010
Posts: 8
Default

Quote:
Originally Posted by billstevens View Post
Also, sorry, does anyone know how to filter more than one file at a time with Fastq?
Yes is the answer to your question as quoted above.
You might have meant to ask how: I usually filter one or more fastq files using the fastx toolkit wrappers in our local Galaxy which fires off jobs to SGE so I can do 'more than one file at a time' - but YMMV as it always does with these things.
fubar is offline   Reply With Quote
Reply

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 06:21 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO