User: Affan

gravatar for Affan
Affan290
Reputation:
290
Status:
Trusted
Location:
Canada
Last seen:
3 years, 11 months ago
Joined:
6 years, 5 months ago
Email:
a******@gmail.com

about me

Posts by Affan

<prev • 61 results • page 1 of 7 • next >
0
votes
1
answer
4.1k
views
1
answers
Comment: C: How to get gene names from CpG islands coordinates with R/Bioconductor
... Can I get a copy of your dataframe? I am looking for Cpgislands in mm9 for my analysis, but don't really know how or where to get the data. If you could save your dataframe as a .Rds file (R binarization), then I can download it. Thanks   ...
written 4.0 years ago by Affan290
1
vote
1
answer
2.0k
views
1
answer
interpreting FIMO results - p value and q value
... I used FIMO to scan promoter regions (defined as 10,000 upstream from TSS) only on chromosome 1 of mm9. The results can be viewed here: http://nbcr-222.ucsd.edu/opal-jobs/appFIMO_4.10.01429210665330517302090/fimo.html I have a couple of questions: 1) For each gene ('sequence name'), it finds a hit ...
position weight matrix motif written 4.2 years ago by Affan290
0
votes
1
answer
1.6k
views
1
answers
Answer: A: calculating promoter region from TxDb for a negative strand gene
... Consider the mailing list questions/answers here: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/promoter$20negative$20strand/genome/EjniLTfREQU/-5_cOndwfSIJ or search for "promoter negative strand" in the mailing list. The answer is that yes, for a gene on the negative strand, ...
written 4.2 years ago by Affan290
0
votes
1
answer
1.6k
views
1
answer
calculating promoter region from TxDb for a negative strand gene
... I am working on a R script that retrieves promoter regions for genes. My question isn't about the specific programming, but in a general biology sense. Consider the gene given to me below by TxDb 99889 chr3 [ 84299986, 85691440] - | 99889 This gene on chr3 (mm9)  is on t ...
strandness written 4.2 years ago by Affan290
0
votes
1
answer
1.9k
views
1
answers
Comment: C: downloading annotated mouse genome
... Thanks, I think this will be easier to use than biomart. Although I'll probably go ahead and use biomart as a "double check"/control. Do you know if TxDb.Mmusculus.UCSC.mm9.knownGene contains RefSeq or Ensembl genes? I also use BSgenome.Mmusculus... instead of TxDb.Musculus... Are they the same? (n ...
written 4.2 years ago by Affan290
0
votes
1
answer
1.9k
views
1
answer
downloading annotated mouse genome
... I want to download the mouse genome (mm9) with some basic annotations: Intergenic region, promoter region, TSS, gene start, gene end, CpG islands and so on. Basically, I have split up the genome (mm9) into 200bp bins. Each bin has some characteristic associated with it (mainly histone modifications ...
genome written 4.2 years ago by Affan290 • updated 4.2 years ago by Devon Ryan90k
0
votes
4
answers
5.2k
views
4
answers
Comment: C: what is the motivation behind Pol2 chip-seq data?
... What is the importance of DNase hypersensitivity track? And what do you mean by false-positives? Sorry I am a math major and just dived into bioinformatics for my MSc research. ...
written 4.3 years ago by Affan290
1
vote
2
answers
1.2k
views
2
answers
an introduction to GO annotations
... I have the mouse genome split into 1000 bp bins. For each bin, I'd like to know how far is it from the nearest gene. A question I posted yesterday got the answer of using biomart (and its R package biomaRt). Going through biomart, I am a bit confused about the GO ontology terms: Consider the followi ...
gene ontology written 4.3 years ago by Affan290 • updated 4.3 years ago by Reema Singh150
4
votes
4
answers
5.2k
views
4
answers
what is the motivation behind Pol2 chip-seq data?
... I am reading a few papers on histone modifications where the data comes from chip-seq experiments. But  most if not all of the papers also get data on RNA polymerase 2. I see why we chip-seq histone modifications. It gives us the positions of these modifications within the genome and based on gene ...
sequence chip-seq written 4.3 years ago by Affan290 • updated 4.3 years ago by mikhail.shugay3.3k
3
votes
1
answer
1.0k
views
1
answer
tools for gene annotation
... I have data from the tool ChromHMM.  What it does is split up the genome/chr into  bins (say 200bp) and assign each bin a state (for those interested, the assignment is based on an observation sequence which are the combination of histone modifications - see Earnst/Kellis 2009 paper).   The data lo ...
go analysis written 4.3 years ago by Affan290 • updated 4.3 years ago by Michael Dondrup46k

Latest awards to Affan

Popular Question 4.3 years ago, created a question with more than 1,000 views. For Chip-sequencing of histone modifications
Appreciated 4.4 years ago, created a post with more than 5 votes. For How can I create a more accurate PWM?
Student 4.5 years ago, asked a question with at least 3 up-votes. For How can I create a more accurate PWM?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1461 users visited in the last hour