User: ognjen011

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ognjen011190
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Posts by ognjen011

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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 9 hours ago by ognjen011190
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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 2 days ago by ognjen011190
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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 18 days ago by ognjen011190
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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 18 days ago by ognjen011190
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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 5 months ago by ognjen011190
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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 5 months ago by ognjen011190
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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 6 months ago by ognjen011190 • updated 4 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 6 months ago by ognjen011190 • updated 6 months ago by mrals8950
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Comment: C: Alternative splicing convention
... I am asking about those two figures. ...
written 7 months ago by ognjen011190
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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 7 months ago by ognjen011190 • updated 7 months ago by RamRS24k

Latest awards to ognjen011

Popular Question 1 day ago, created a question with more than 1,000 views. For Problems while reheadering BAM with Samtools 1.3.1
Popular Question 5 months ago, created a question with more than 1,000 views. For Problems while reheadering BAM with Samtools 1.3.1
Popular Question 5 months ago, created a question with more than 1,000 views. For Spot Group in SRA
Popular Question 6 months ago, created a question with more than 1,000 views. For Spot Group in SRA
Popular Question 8 months ago, created a question with more than 1,000 views. For FastQC and adapters
Supporter 11 months ago, voted at least 25 times.
Appreciated 2.1 years ago, created a post with more than 5 votes. For BED files for SRA open projects
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For BED files for SRA open projects
Student 2.1 years ago, asked a question with at least 3 up-votes. For BED files for SRA open projects

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