User: ankitplusplus
ankitplusplus • 30
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- 1 year, 4 months ago
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- 2 years, 11 months ago
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Posts by ankitplusplus
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... How much percentage of contacts are similar between single cell Hi-C and population Hi-C. And also how much variation or similarity is there between nuclei of cells in terms of chromatin contacts. ...
written 17 months ago by
ankitplusplus • 30
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... Hello everyone,
Does anyone know, is there any data of nucleosome positioning available of different cell types for example GM12878, T47D, erythroblast, HeLa-S3 etc.
Thank you. ...
written 18 months ago by
ankitplusplus • 30
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... Hi, I was reading some articles where CTCF binding sites co-occur with cohesin (RAD21) binding site with 60-80% in any particular cell. I wanted to know what fraction of these binding sites found inside chromatin interacting regions and outside chromatin interacting regions. What I understand from C ...
written 20 months ago by
ankitplusplus • 30
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... Hi,
Does anyone know any Transcription factor or motif region which occur in the nucleosome-free region in one cell type and nucleosome-bound region in any other cell type? ...
written 22 months ago by
ankitplusplus • 30
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... I am calculating probability of contacting pair using zhang and wolynes 2015 PNAS method
p(i,j) =min(1,C(i,j)/min(ni,nj))
where ni = max[ C(i-4, i), C(i-3,i), ..., C(i,i+2), C(i,i+3) ]
C(i,j) is the contact frequency of pairs.
So, i have a doubt that what value of C(i,i) should i used for calculat ...
written 2.6 years ago by
ankitplusplus • 30
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... Thanks for the answer. My bin size is 40 kb. You are correct that diagonal should be the highest value. But for finding the true contact pairs should i use diagonal value as it is or should i put 0 in diagonal. I have a confusion about that. ...
written 2.6 years ago by
ankitplusplus • 30
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... Hi everyone,
In Hi-C contact matrix, i see non zero values in diagonal. What is the meaning of self contacting.
Should i ignore the diagnoal for further calculation.
Thanks
...
written 2.6 years ago by
ankitplusplus • 30
• updated
2.6 years ago by
Anton Goloborodko • 250
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Comment:
C: seed sequences of human miRNA
... Thanks a lot for your answer. ...
written 2.7 years ago by
ankitplusplus • 30
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... Hi,
Can anybody help me to find out the list of seed sequences of human miRNA. Is there any tool, database or article where i can get all the seed list.
Thanks. ...
written 2.7 years ago by
ankitplusplus • 30
• updated
2.7 years ago by
ashraf.bioinfo • 10
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... Hi,
I have some list of human genes and i wanted to find all transcription factor associated with these genes.
What software tools, database i can used for finding such regulatory TF. ...
written 2.7 years ago by
ankitplusplus • 30
• updated
2.7 years ago by
zwdzwd • 120
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20 months ago,
created a question with more than 1,000 views.
For seed sequences of human miRNA
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