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Old 06-03-2011, 09:10 AM   #1
madsaan
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Exclamation FASTQC for checking quality of 120 bp reads

Hello,

I am trying to check the quality of my GA11 illumina reads that are 120bp long and I am getting very low median values after the 70th bp.I would like to know if FASTQC is a reliable tool for long reads or is there something els available online?
Your help will be greatly appreciated.

Thanks,
Madhu
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Old 06-03-2011, 11:07 AM   #2
mgogol
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I think fastqc works fine for 120 base reads.
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Old 06-06-2011, 01:54 PM   #3
robs
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If you want to compare it to results of alternative programs, try e.g. PRINSEQ (http://prinseq.sourceforge.net/).

If you do a search, you will find this one as well:
http://seqanswers.com/forums/showthread.php?t=10359
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Old 06-06-2011, 11:17 PM   #4
simonandrews
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The length of the reads doesn't really matter to FastQC, it's just reporting on the qualities which are already in your data. On the project web page you can see results for 454 and PacBio runs which are much longer than this.

For reads over 75bp it will start grouping bases later in your reads so as to not make really wide plots, this can make it look like the quality is declining more quickly because the x-axis is compressed. If you really want to see every base in a plot you can disable this behaviour using the --nogroup option.
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Old 06-06-2011, 11:17 PM   #5
simonandrews
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The length of the reads doesn't really matter to FastQC, it's just reporting on the qualities which are already in your data. On the project web page you can see results for 454 and PacBio runs which are much longer than this.

For reads over 75bp it will start grouping bases later in your reads so as to not make really wide plots, this can make it look like the quality is declining more quickly because the x-axis is compressed. If you really want to see every base in a plot you can disable this behaviour using the --nogroup option.
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