Moderator: Kevin Blighe
Kevin Blighe ♦ 37k
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'Incrocio le dita e spero'
'There are mountains in our way... but we climb a step every day'
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Developer / Maintainer of Bioconductor packages:
Posts by Kevin Blighe
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... Double-check the version that you are using. Note the release notes:
RSeQC v2.6.1
Fix bug in “junction_annotation.py” in that it would report some “novel splice junctions” that don’t exist in the BAM files. This happened when reads were clipped and spliced mapped simultaneously.
*[source: h ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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... I am not familiar with the program, however, the default for depth appears to be 5:
--min_depth MIN_DEPTH Minimum mean depth to flag as dubious allele call (default 5)
Taken from: https://github.com/katholt/srst2
...
written 16 hours ago by
Kevin Blighe ♦ 37k
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... All RNA-seq count data is shifted toward zero, so, that is expected. RNA-seq counts follow a negative binomial distribution. I don't believe that production of FPKM expression values results in an overall change from this data distribution. A transformation of normalised counts via, e.g., variance-s ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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Comment:
C: HMM and NGS mapping
... Can you elaborate on what you mean by the 'reference transcript HMM profiles'? ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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... Yes, you would mainly want the following EUR populations, i.e.:
- CEU, Utah Residents (CEPH) with Northern and Western European
Ancestry
- TSI, Toscani in Italia
- GBR, British in England and Scotland
The others are:
- FIN, Finnish in Finland
- IBS, Iberian Population in Spain
People fro ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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Comment:
C: Population Private SNPs
... ^^ It does indeed seem to be as straight forward as how zx8754 describes. The allele frequency data can be used to infer alleles that are only present in one population group or another. If I was actively working on this, I would spend some time to get the 1000 Genomes data into a single BCF and als ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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... Looks like your data has '*Category*' whereas the function looks for '*category*' (small 'c').
You should also look into your objects to see how they look. It is a good habit to have. For example:
head(genelist)
head(david)
As a side note, I posted a tutorial for plotting DAVID results: h ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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... Yes, to further elaborate on Erin's final point, as an example, recent *in silico* prediction tools have compared mutation frequencies against random mutation backgrounds and/or 'derived' alleles that have become fixed (conserved) in the human lineage when compared to our recent ape ancestor. If you ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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... I think that you need to clear up what your file extensions mean.
With your first command, you have specified:
-O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz
`-O b` does not output a bgzipped VCF file, as your output filename (*$x.multiallelicIndelsRemoved.1240positions.vcf.bgz*) ...
written 16 hours ago by
Kevin Blighe ♦ 37k
• updated
15 hours ago by
WouterDeCoster ♦ 36k
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Comment:
C: Interpreting DEseq2 results
... Okay, cool. ...
written 16 hours ago by
Kevin Blighe ♦ 37k
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