User: Sama

gravatar for Sama
Sama30
Reputation:
30
Status:
New User
Location:
Last seen:
1 day, 17 hours ago
Joined:
1 year, 4 months ago
Email:
d*********@gmail.com

Posts by Sama

<prev • 19 results • page 1 of 2 • next >
0
votes
2
answers
119
views
2
answers
Comment: C: How to find the unique list of mismatches of reads with the reference genome
... This is 5 first lines of running your command on my data: 3242056 Escherichia 0 A 3435134 Escherichia 0 C 3169976 Escherichia 0 G 85 Escherichia 0 N 2952800 Escherichia 0 T It is weird if the frequency of A in first position is 3242056. Also the third column numbers range is 0-100 but the r ...
written 7 days ago by Sama30
0
votes
2
answers
119
views
2
answers
Comment: C: How to find the unique list of mismatches of reads with the reference genome
... Thank you for your reply. I have a question. What are first and third columns? ...
written 7 days ago by Sama30
5
votes
2
answers
119
views
2
answers
How to find the unique list of mismatches of reads with the reference genome
... Hi, I have Illumina reads and a reference genome. I aligned reads to the genome and I have .bam and .sam files. I want the list of the mismatches of the reads with the reference genome but if one mismatch happened in multiple reads, I want it to be reported only once. For example if two reads have ...
genome next-gen alignment written 8 days ago by Sama30 • updated 8 days ago by pfs90
0
votes
0
answers
273
views
0
answers
How to find cell-specific enhancer-promoter interactions?
... I extracted enhancer-promoter interactions of Gm12878, HMEC cells from Hi-C data and I want to have the cell specific interactions of each cell line. I assumed, when in two interactions their promoters are overlapping and their enhancers are overlapping as well, I considered them to be the same. Usi ...
interactions gene regulation cell specific written 7 months ago by Sama30
0
votes
1
answer
429
views
1
answers
Comment: C: Computational Research Topics in Transcriptional Gene Regulation
... Thank you. I have changed my subject and I do not study bacteria anymore. ...
written 15 months ago by Sama30
1
vote
0
answers
334
views
0
answers
Why we need computational methods for predicting DHS activity?
... In [this paper (Basset)][1], the authors try to predict DHS activity. My question is that why they predict DHS? Is experimentally extracting DHS activity expensive? They just explained that it is useful to have DHS activity but they did not mentioned what is the point of having a computational appro ...
gene dhs noncoding regulation genomics written 15 months ago by Sama30
0
votes
0
answers
366
views
0
answers
Benefits of Having Enhancer-Promoter Interactions
... I have been reading some papers about Enhancer-Promoter Interactions Prediction such as: - Roy, Sushmita, et al. "A predictive modeling approach for cell line-specific long-range regulatory interactions." Nucleic acids research 43.18 (2015): 8694-8712. - He, Bing, et al. "Global view of enhancer– ...
prediction gene enhancer interactions promoter written 15 months ago by Sama30
2
votes
1
answer
429
views
1
answer
Computational Research Topics in Transcriptional Gene Regulation
... I want to find a research topic in Transcriptional Gene Regulation. My background is Computer Science so I am not familiar with general important topics in this area. I guess one of the problems is Predicting Enhancer Target Gens. What computational problems exist related to Transcriptional Gene Re ...
gene regulation genomic enhancer transcription written 15 months ago by Sama30 • updated 15 months ago by natasha.sernova2.5k
0
votes
0
answers
376
views
0
answers
Comment: C: What are the examples of mixture of closely related bacterial strains?
... So in every bacterial population there are very similar strains? What are the benefits of separating those close strains from each other? For example, I know that in order to choose the right treatment for a some diseases it is necessary to be able to separate closely related bacteria correctly. Wha ...
written 15 months ago by Sama30
1
vote
0
answers
376
views
0
answers
What are the examples of mixture of closely related bacterial strains?
... I know that mixed infections contain mixture of a few unrelated strains of the same bacterial species ([source][1]). What are the other examples of this kind of mixture? Actually, I want to know where mixture of bacterial strains (similar strains with 100-10000 bp variations from each other) can b ...
mixture bacterial data strains written 15 months ago by Sama30

Latest awards to Sama

Great Question 7 months ago, created a question with more than 5,000 views. For What is the illumina sequencing error rate?
Popular Question 13 months ago, created a question with more than 1,000 views. For What is the illumina sequencing error rate?
Supporter 15 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1284 users visited in the last hour