Moderator: Damian Kao
Damian Kao ♦ 15k
- Reputation:
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- http://blog.nextgeneti...
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- Joined:
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Bioinformatician at Janelia Research Campus.
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... Even if multiple samples were mixed together in the depth of cov reporting, it should not show this distribution. Multi-sample mix should show a smooth histogram with potentially multiple peaks. Maybe try using samtools stats' depth of coverage info for plotting and see if you get the same thing. Pe ...
written 23 months ago by
Damian Kao ♦ 15k
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... This looks like a histogram plotting issue where it is binning the depth values in a skewed way. ...
written 23 months ago by
Damian Kao ♦ 15k
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... I don't think it is possible to differentiate between batch effects and biological effect in this case. If you performed the experiment with biological conditions side by side in two batches, then you can try to look for batch effects. ...
written 2.0 years ago by
Damian Kao ♦ 15k
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... As far as I know, Tophat2 uses Bowtie2 in several stages. The initial stages (mapping to transcriptome and genome) are performed to get all the unmapped reads. The unmapped reads are then splitted and mapped separately to check if they span an intron.
How bowtie2 is parameterized in Tophat2 is like ...
written 2.0 years ago by
Damian Kao ♦ 15k
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... Are your fastqs paired in the same order already? Do you have entries where one of the pair (forward or reverse) is missing? ...
written 2.0 years ago by
Damian Kao ♦ 15k
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... Everyone who participates on this website by answering questions are doing this voluntarily. We do not get paid or benefit from this. We all have other responsibilities in our professional and personal lives. We are not here to act as your professor or full-time teacher.
I understand that learning ...
written 2.0 years ago by
Damian Kao ♦ 15k
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... As with most interval operations, bedtools has a command for it:
https://bedtools.readthedocs.io/en/latest/content/tools/flank.html ...
written 2.3 years ago by
Damian Kao ♦ 15k
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Comment:
C: SNP calling from BAM file
... Can you please post the command you used and the error message. ...
written 2.3 years ago by
Damian Kao ♦ 15k
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... Packages like edgeR and DESeq2 don't actually transform the counts for DE analysis. A normalization factor is calculated and then used in the DE test. There are good information in the absolute counts for each gene. Standardization is not used, otherwise that information would be lost. ...
written 2.4 years ago by
Damian Kao ♦ 15k
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Comment:
C: Abyss run time
... What's the estimated genome size of your organism? And how many reads do you have? ...
written 2.4 years ago by
Damian Kao ♦ 15k
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