User: ognjen011

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ognjen011200
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Posts by ognjen011

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ROC for a family of repeated variables
... Suppose I have a continuous covariate like age, and I want to use it for RNA-Seq quantification, but in the categorical binary form, and I want to find the optimal threshold. I understand that this optimality can be defined depending on the presence of the grouping outcome variable. ------ If I hav ...
quantification rna-seq written 3 months ago by ognjen011200
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Comment: C: Local alignment of different lengths in Biopython
... You are correct, I used alignxx which doesn't score INDELs. Please answer the Q so I can accept, and I added that to edit. ...
written 10 months ago by ognjen011200
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Local alignment of different lengths in Biopython
... I am trying to find the optimal local alignment score of a short sequence (50bp) to a reference bacterial genome of several Mbp. When I use Biopython Align module, I always get the score equal to the length of the shorter (query) sequence. For example, with alignxx function: ('--G------------------ ...
alignment written 10 months ago by ognjen011200
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Comment: C: Checking for enrichment of certain kmers
... Essentially it is, and I didn't know that was a category or that those tools existed. Thank you sir, please post that as an answer. ...
written 10 months ago by ognjen011200
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Checking for enrichment of certain kmers
... As a general problem, I frequently have some genomic locations, intervals or probes which are in some way selected from the remainder. For example, in ChipSeq I could have a number of intervals where peaks occurred. If I hypothesize that they all have a common motif, a pattern of some sort, is there ...
sequence written 10 months ago by ognjen011200
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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 15 months ago by ognjen011200
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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 15 months ago by ognjen011200
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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 16 months ago by ognjen011200 • updated 14 months 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 16 months ago by ognjen011200 • updated 16 months ago by mrals8950
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Comment: C: Alternative splicing convention
... I am asking about those two figures. ...
written 17 months ago by ognjen011200

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Popular Question 7 months ago, created a question with more than 1,000 views. For Problems while reheadering BAM with Samtools 1.3.1
Popular Question 10 months ago, created a question with more than 1,000 views. For Problems while reheadering BAM with Samtools 1.3.1
Popular Question 15 months ago, created a question with more than 1,000 views. For Problems while reheadering BAM with Samtools 1.3.1
Popular Question 15 months ago, created a question with more than 1,000 views. For Spot Group in SRA
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Appreciated 2.9 years ago, created a post with more than 5 votes. For BED files for SRA open projects
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Student 2.9 years ago, asked a question with at least 3 up-votes. For BED files for SRA open projects

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