User: Affan
Affan • 290
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Posts by Affan
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... 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
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written 5.4 years ago by
Affan • 290
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... 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 ...
written 5.5 years ago by
Affan • 290
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... 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 5.5 years ago by
Affan • 290
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... 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 ...
written 5.5 years ago by
Affan • 290
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... 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 5.6 years ago by
Affan • 290
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... 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 ...
written 5.6 years ago by
Affan • 290
• updated
5.6 years ago by
Devon Ryan ♦ 97k
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... 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 5.6 years ago by
Affan • 290
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... 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 ...
written 5.6 years ago by
Affan • 290
• updated
5.6 years ago by
Reema Singh • 160
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... 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 ...
written 5.6 years ago by
Affan • 290
• updated
5.6 years ago by
mikhail.shugay ♦ 3.4k
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... 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 ...
written 5.6 years ago by
Affan • 290
• updated
5.6 years ago by
Michael Dondrup ♦ 47k
Latest awards to Affan
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5.6 years ago,
created a question with more than 1,000 views.
For Chip-sequencing of histone modifications
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5.8 years ago,
created a post with more than 5 votes.
For How can I create a more accurate PWM?
Student
5.8 years ago,
asked a question with at least 3 up-votes.
For How can I create a more accurate PWM?
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