User: kuckunniwid

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kuckunniwid20
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Posts by kuckunniwid

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Enrichment platforms for 1000GP exome data
... The answer is actually here: http://www.internationalgenome.org/category/exome/ ...
written 5 days ago by kuckunniwid20
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Comment: C: Enrichment platforms for 1000GP exome data
... thank you a lot. well it seems that I am not smart enough, but can you point me to the name of the spreadsheet / name of the column that contains this information? Of course I've checked this spreadsheet and I still do not see where this information is stored. ...
written 5 days ago by kuckunniwid20
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Enrichment platforms for 1000GP exome data
... Dear all, I've found a lot of information about different samples and sequencing platforms from 1000GP, however I have not found the list matching between "sample ID -> enrichment platform used for WES sequencing", and this is crucial for me since I need to work only with on-target reads that ca ...
data wes written 5 days ago by kuckunniwid20
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Answer: A: Inconsistent Coverage on X chromosome between genders
... The answer to the problem seems to have 2 parts: 1) in case you do not filter reads with high probabilitiy of misalignment, you will have a lot of "background" reads on your genome. That means that erroneous reads from all the genome will randomly map to some locations. It makes a huge effect on of ...
written 10 months ago by kuckunniwid20
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Comment: C: Inconsistent Coverage on X chromosome between genders
... I think this bias actually exists. I was thinking that strict mappability filtering will eliminate this bias, but finally no, the ratio is still 1.93, not 2. So I guess there is no other explanation except saturation of probes... ...
written 10 months ago by kuckunniwid20
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Comment: C: Inconsistent Coverage on X chromosome between genders
... My colleague who actually knows what happens in Agilent enrichment kits told me that there are much more probes than DNA so the effect should be minor. But we'll know tomorrow when the results will be finished. ...
written 10 months ago by kuckunniwid20
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Comment: C: Inconsistent Coverage on X chromosome between genders
... Thanks! I will close when the issue will be finally solved (hopefully tomorrow), I mistakenly reported it as "answered" while there is still some uncertainty here. ...
written 10 months ago by kuckunniwid20
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Comment: C: Inconsistent Coverage on X chromosome between genders
... I finally understood your concerns and it makes sense. I will try to include this "saturation" as the parameter in my estimations. But such drastic change in number of reads was partially explained by the "uncertainly" mapped reads. I excluded all reads with MAPQ < 2 and I had median ratio of 1.9 ...
written 10 months ago by kuckunniwid20
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Comment: C: Inconsistent Coverage on X chromosome between genders
... I expect the number of reads on X chromosome be doubled for females comparing to males regardless are they on-target or off-target. This is a common assumption that arise from the fact that we have 2 copies of the region in females and 1 copy for males. ...
written 10 months ago by kuckunniwid20
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Comment: C: Inconsistent Coverage on X chromosome between genders
... Yeap, but technically, if you have 1 copy or 2 copies - the processes should be similar for both of them and in the end we will have ratio close to 2 anyway. ...
written 10 months ago by kuckunniwid20

Latest awards to kuckunniwid

Scholar 10 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders

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