User: ognjen011

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ognjen011170
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Posts by ognjen011

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Comment: C: Proband of CEPH Family 1463
... These are the famous Illumina Platinum genomes, I was hoping there was some common knowledge involved. But I am glad you are perceiving the same weirdness as I did. ...
written 10 weeks ago by ognjen011170
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Proband of CEPH Family 1463
... Maybe I have some terminology wrong, or I misunderstand something about pedigrees, but isn't the proband the starting point of a study? Why is he not included in the cohort? If you look at the link: https://www.coriell.org/0/Sections/Collections/NIGMS/CEPHFamiliesDetail.aspx?PgId=441&fam=1463&a ...
pedigree written 10 weeks ago by ognjen011170
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(Closed) Cloning after PCR, then sequencing
... The following paper has the following section on methylation in methodology: https://www.sciencedirect.com/science/article/abs/pii/S0143400415008991?via%3Dihub DNA methylation analysis Genomic DNA samples obtained from the normal and PE placentas were purified using DNAzol (Invitrogen). Pur ...
cloning sequencing methylation pcr written 3 months ago by ognjen011170 • updated 6 weeks ago by Biostar ♦♦ 20
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Distance of promoter from TSS
... Although this question is found around in some forms, I am wondering about a specific example. There is an undecided distance around the TSS in which one can look for promoters, and that is usually several kb upstream and some distance in the first exome. I get the difficulty in giving the precise ...
annotation gff promoter transcription written 3 months ago by ognjen011170 • updated 3 months ago by mrals8930
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Comment: C: Alternative splicing convention
... I am asking about those two figures. ...
written 4 months ago by ognjen011170
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Alternative splicing convention
... I am reading the [`SUPPA2` github page][1] and can't truly understand the symbolic conventions for the events. What is a dash and what is a colon? Do they have distinct, constant meanings? For skipping exons (e1-s2:e2-s3) colon seems to mean SKIP, while for alternative 5' it means OR, and for some o ...
splicing rna-seq written 4 months ago by ognjen011170 • updated 4 months ago by RamRS23k
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Answer: A: Relatedness vs relatedness2 from vcftools give different results
... Hi! The --relatedness method based on doi:10.1038/ng.608 is only appropriate for large cohorts. Although this is not properly indicated in the [documentation][1], it is revealed in questions on [SourceForge][2]. Looking at the paper equation (6) in supplementary, the values of AF near 0 or 1 make t ...
written 4 months ago by ognjen011170
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Comment: C: Genotyping diploid organisms from Sanger AB1 files
... This is a very valid concern. If all fails, it will be a nice way to screen or double-check. ...
written 5 months ago by ognjen011170
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Genotyping diploid organisms from Sanger AB1 files
... Hi! I am trying to automate variant calling on human short exons sequenced with Sanger method. I have the ab1 files, and I want to automate the process for clinical geneticists. The program should be free, I understand that is a huge limitation. Also, it needs to register INDELS in addition to SNPs ...
variant-calling sanger written 5 months ago by ognjen011170 • updated 5 months ago by trausch1.4k
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Connection of SNPs to Enzyme activity - database or tool
... Is there a resource - database or prediction tool - that maps SNPs to changes in enzyme activity? This could either be achieved through prediction of direct effects on structure, or the measurement of products. Either way works fine as long as it elucidates function effects. Tools like PolyPhen2 d ...
proteomics snp written 6 months ago by ognjen011170

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