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10-04-2012, 01:10 PM
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#1 |
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Member
Location: US Join Date: Mar 2012
Posts: 36
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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!!! |
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10-04-2012, 01:21 PM
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#2 | |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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Quote:
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10-04-2012, 01:50 PM
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#3 |
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Member
Location: Seattle, WA Join Date: Mar 2009
Posts: 87
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You can use fastx to filter based on your desired quality score.
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10-08-2012, 04:03 PM
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#4 |
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Senior Member
Location: Baltimore Join Date: Mar 2012
Posts: 120
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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?? |
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10-09-2012, 08:56 AM
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#5 |
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Senior Member
Location: Baltimore Join Date: Mar 2012
Posts: 120
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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.
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10-09-2012, 03:48 PM
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#6 |
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Senior Member
Location: Baltimore Join Date: Mar 2012
Posts: 120
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Also, sorry, does anyone know how to filter more than one file at a time with Fastq?
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10-09-2012, 04:18 PM
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#7 | |
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Crusty old bioinformatician
Location: Melbourne, Australia Join Date: Oct 2010
Posts: 8
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Quote:
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. |
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