Originally posted by sowmyai
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Originally posted by sowmyai View PostThanks.
In that case, I don't understand how my data could fail the Per Base sequence test(miserably at that - the blue line dips sharply after 35 bp - these are 76 bp reads) and pass the "Per Sequence" test. Thanks for your patience.
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I was not so much concerned about the pass/fail from the software.
When I say "Passed the Per Sequence quality test" I meant that the histogram peaks very steeply at 34. How can most reads have an average quality of 34 while the individual base qualities are very poor ?
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Originally posted by sowmyai View PostI was not so much concerned about the pass/fail from the software.
When I say "Passed the Per Sequence quality test" I meant that the histogram peaks very steeply at 34. How can most reads have an average quality of 34 while the individual base qualities are very poor ?
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Originally posted by simonandrews View Post... the per-sequence quality check won't actually issue a warning or a fail - it just shows you the results and lets you decide. There are a couple of tests like this (the GC plot I think is another one). ...
Great software, btw. Thanks for solid work.
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This is a really awesome program. I really like how easy it is to use and how clearly it summarizes everything.
One thing, I cant seem to copy and paste out overrepresented sequences. This would be very useful as the first thing I want to do it figure out where the reads come from.
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Originally posted by lparsons View PostOne suggestion would be to change the icon for tests that do not issue a warning or a fail to a blue "i" icon for info instead of the green check mark. That would make it obvious to people that there is no check for this test.
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Originally posted by sowmyai View PostHow can most reads have an average quality of 34 while the individual base qualities are very poor ?
In effect this means that the scale on the left of the plot was shifted downwards by whatever the difference in these values was. For Illumina fastq files they were off by 2 Phred units, but it could have been more in other formats.
This will be fixed in the next (impending) release.
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Originally posted by Bruins View PostHow would you like to be cited? It is for a report that will (most likely) not be published.
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FastQC v0.4.2 released
I've just put FastQC v0.4.2 up on our website.
This fixes the per-base quality plot bug which caused the y-axis to show an offset scale. It also adds more strict parsing of FastQ files to spot incorrectly formatted files, and more cleanly distinguish base called and colorspace files.
I've also now added fail / warn checks to all of the QC modules and improved some of the existing checks which would fail for libraries with unusual GC contents. As part of this I've added a modelled distribution into the per-sequence GC plot so you can see how well your observed distribution fits.
Finally, I've changed the scaling on the graphs in the HTML reports so that wider graphs will be generated for libraries with long reads so you don't get squashed graphs.
You can get the new version from:
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
[If you don't see the new version of any page hit shift+refresh to force our cache to update]Last edited by simonandrews; 07-26-2010, 03:43 AM.
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Originally posted by simonandrews View PostI've just put FastQC v0.4.2 up on our website.
There appears to be a bug introduced in v0.4.2 related to the "Total Sequences" count reported in the Basic Statistics. The new version consistently under reports the number of reads in the file. Previous versions correctly reported the count.
Looking at the documentation I see that there was a planned feature for sampling just a subset of reads in a file and then reporting an estimate of the total number of reads. Could this have something to do with it?
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Originally posted by kmcarr View PostThere appears to be a bug introduced in v0.4.2 related to the "Total Sequences" count reported in the Basic Statistics. The new version consistently under reports the number of reads in the file. Previous versions correctly reported the count.
Originally posted by kmcarr View PostLooking at the documentation I see that there was a planned feature for sampling just a subset of reads in a file and then reporting an estimate of the total number of reads. Could this have something to do with it?
Thanks for spotting this. I'll put out v0.4.3 later today with a fix for this problem.
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