User: emmanouil.a

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emmanouil.a30
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Posts by emmanouil.a

<prev • 18 results • page 1 of 2 • next >
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Comment: A: bcftools roh with -e option... never finish
... Hi, any help please! ...
written 27 days ago by emmanouil.a30
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CNVkit: call sex chr - germline analysis
... 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 ...
next-gen written 5 weeks ago by emmanouil.a30 • updated 5 weeks ago by _r_am32k
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Comment: C: Split reads (fastq) x read barcode sequence (no barcode in RG)
... Many thanks, I will try! ...
written 7 weeks ago by emmanouil.a30
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Split reads (fastq) x read barcode sequence (no barcode in RG)
... 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 ...
next-gen sequence written 7 weeks ago by emmanouil.a30 • updated 7 weeks ago by GenoMax94k
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CNVkit intervarls questions
... 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 ...
cnvkit written 7 weeks ago by emmanouil.a30
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Comment: C: wes uncovered regions: how to link the gene name to the uncovered genome coordin
... Hi, already done this! ...
written 12 months ago by emmanouil.a30
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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.a30
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bcftools roh with -e option... never finish
... 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 ...
roh bcftools written 12 months ago by emmanouil.a30
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wes uncovered regions: how to link the gene name to the uncovered genome coordinates
... 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 ...
gene next-gen written 12 months ago by emmanouil.a30
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hg38 Ig regions
... 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 ...
assembly sequence written 21 months ago by emmanouil.a30

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