User: emmanouil.a
emmanouil.a • 30
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Posts by emmanouil.a
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... Hi, any help please!
...
written 27 days ago by
emmanouil.a • 30
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... Hi,
I have 55 males and 45 females and I ran those groups separately and in both cases using a flat reference.
I'm using the following codes
1)
cnvkit.py access ${hg38} -o acces_hg38.bed
cnvkit.py target hg38_design_1-22-X.bed --split --annotate ${flat} -o targets.bed
cnvkit.py an ...
written 5 weeks ago by
emmanouil.a • 30
• updated
5 weeks ago by
_r_am ♦ 32k
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... Many thanks, I will try! ...
written 7 weeks ago by
emmanouil.a • 30
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136
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... Hi,
I have a target PCR basic custom library with a unique initial barcode (IonTorrent barcode). For example, I amplified two regions... the two regions start with a common sequence "linker" and then they have a "region barcode", like
AAAAAAAAnBBBBBBBnnnnnnnnnn (first_region:AAA...=linker, BBB ...
written 7 weeks ago by
emmanouil.a • 30
• updated
7 weeks ago by
GenoMax ♦ 94k
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... Hi,
I have a Whole Exome Sequencing baits design of 84Mb.
Why I need to create an access file (access.hg38.bed) if I already have the bait file?
When I run target command
> cnvkit.py target --annotate ${flat_file} --split ${baits_file} -o
> "hg38_baits_annot_split.bed"
the design now is 8 ...
written 7 weeks ago by
emmanouil.a • 30
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... Hi, already done this! ...
written 12 months ago by
emmanouil.a • 30
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Comment:
A: hg38 Ig regions
... Many thanks for you answer, in this way I found that I need!
Best! ...
written 12 months ago by
emmanouil.a • 30
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... Hi,
I have 25 vcf with only GT values, and I merged them with "vcf-merge ${all_samples}"
after merge I have some situations like the following where not all samples have a GT... in general is normal ...
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT wes001 wes002 wes003 ...
written 12 months ago by
emmanouil.a • 30
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... Hi,
I have a big list of genes and I found the uncovered regions (0X, WES data). The point is that I have the uncovered genome coordinates but I do not know the related gene names of those coordinates...
In "Genome Browser -> Tools -> Table Browser": I take the coordinates of all exons of th ...
written 12 months ago by
emmanouil.a • 30
9
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844
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7 follow
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... Hi,
I'm looking for the Immunoglobulin regions coordinates in hg38 assembly. I want to exclude them from my CNV analysis.
I know the hg19 regions but I do not want just to liftover them.
Many thanks ...
written 21 months ago by
emmanouil.a • 30
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