User: alteralex

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alteralex40
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Posts by alteralex

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Scaning A Genome With Simple Markov Model To Find A Motif
... It seems that fimo (from MEME) needs a PWM, not a Markov model... ...
written 6.0 years ago by alteralex40
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Answer: A: How To Quantify The Significance Of The Conservation Of Dna Fragments
... For those that are interested in my question, I think I have found an answer from David Haussler's paper: http://genome.cshlp.org/content/15/8/1034.abstract ...
written 6.0 years ago by alteralex40
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Answer: A: How Are Rna-Seq Transcripts Assigned?
... Thank you Malachi, Mikael and Andrew for the excellent input. I have a very similar problem in my research: I want to calculate the single-nucleotide resolution abundance for each isoforms, so I need to assign fragments to individual isoforms. It sounds to me that Cufflinks may have obtained this in ...
written 6.0 years ago by alteralex40
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Why Tophat Does Not Map Some Reads
... Hi, I am trying to use Tophat for my RNA-seq analysis. I tested my PE reads following three protocols. 1, no reference gene annotation (GTF file) I noticed some PE reads are correctly mapped. The flags are 83 and 163. See an example as the following: M01339:30:000000000-A42G7:1:1101:15690:1356 ...
gtf tophat written 6.0 years ago by alteralex40
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Comment: C: How To Quantify The Significance Of The Conservation Of Dna Fragments
... Thank you bstephenwhite for your input. Indeed the score I have for each base is the PhastCons score. I want to base on these scores to find conserved fragments. And for genome-wide selection, I need a formal way to quantify the significance of the conservation of the fragments I found. ...
written 6.1 years ago by alteralex40
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How To Quantify The Significance Of The Conservation Of Dna Fragments
... I have a genome, and each position has a conservation score. I want to identify the conserved fragments from these scores. A naive way would be to setup two thresholds, one for the conservation score at each base and another one could be the length of the fragments. I want to calculate a P-value or ...
conservation written 6.1 years ago by alteralex40 • updated 4.8 years ago by Biostar ♦♦ 20

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