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Does it seems acceptable (Global GC cotent for the species = 40%)
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Last edited by analyst; 11-28-2011, 01:48 PM. -
Can you attach it to the forum? That site is blocked from here. Also it would be useful to see the per sequence GC plot as well as the per base plot. -
Please do not use that host for images - it has NSFW content displayed prominently, and I have no desire to get sacked for viewing SeqAnswers links in an open plan office.Originally posted by analyst View PostComment
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I understand and apologize. and thanks to the person moderating who posted image correctly
Can anyone please comment on the fastQC findingComment
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I can't see an image reposted. The moderator only removed the original link. We still can't see your data.Comment
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analyst, you may want to look at the following website:
Introduction gives some general information on the FastQC algorithm. For specific information on the modules (what the developers consider as "pass", "warn" and "fail"), see under "Analysis modules" there will be some text files about each module and what their thresholds are.
This is a quote from the section on GC content:
Does this answer your question?Warning
This module issues a warning it the GC content of any base strays more than 5% from the mean GC content.
Failure
This module will fail if the GC content of any base strays more than 10% from the mean GC content."Though it may seem that all's been said and done, originality still lives on" - some unoriginal guy who had nothing better to write as his signature
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Looks acceptable to me.
What concerns you? If it is the low-level but periodic fluctuations in base levels across the read, that has been commented on before in another thread. There the period is three bases per cycle and more regular than what you see here.
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PhillipComment
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Thanks for the comments orr and phillip. Consider me beginner, just wanted to make sure the peaks at certain positions is nothing to worry about. It is more pronounced in the second picture I just posted, at 43. FastQC is warning me but I am not reading too much into it.
Simon, can you see the new picture I just posted, if not, I am also attaching here.Comment
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Okay, the new plot (the second one) is a different story. The G peak at 42 bases may indicate an issue of some sort.
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PhillipComment
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help with fastQC per base sequence content
Hi,
I am a beginner of RNA-seq data analysis. I did fastQC of my samples and I found some variations at the beginning of reads for per base seqence content check. would you please tell me whether it is ok?
Many thanks in advance!Comment
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kmcarr,
Thanks a lot!Comment
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Hello,
I ran FastQC through RNA-seq done on ribodepleted samples and the per base sequence content and per base GC content shows a very heavy bias (If I am correctly interpreting the results). Is this expected in data from ribodepleted RNA. Can this data be used at all?
Please find the image attached. Thanks for your help in advance!Last edited by Aditi Verma; 02-15-2017, 01:52 AM.Comment
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@Aditi: Have you scanned/trimmed this data for presence of Illumina adapters? I wonder if you have a large percentage of adapter dimers (and no real inserts).
I recommend using bbduk.sh from BBMap for this purpose. Search for the thread on bbduk here.Comment
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Looks like about 20-25% of your reads are from adapter dimers.
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PhillipComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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