User: earonesty

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earonesty220
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Posts by earonesty

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Combining quality scores when aligning/assembling
... I spoke to a statistician here. I think a correct'ish answer for ambiguous bases is (after taking the better quality base): E = max(3,((1-e2/2) * e1) / ((1-e1) * e2/2 + (1-e2/2) * e1)) Where e2 is the lower score. And that this algorithm can be used to approximate it without needing to convert to ...
written 4.6 years ago by earonesty220
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Comment: C: Combining quality scores when aligning/assembling
... For mismatches.... min(a,b,max(abs(a-b),3))?   That seems a close approximation.   At least it seems to make sense to me when they are the same (3), and when they are far apart. ...
written 4.6 years ago by earonesty220
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Comment: C: Combining quality scores when aligning/assembling
... Note:  When the bases match, it's a much easier problem.   With an assumption of independence, you can simple add the q scores.   But that this assumption is fundamentally flawed.    For Illumina I use max(a,b)+min(4,min(a,b)) ... when they match.  It's the mismatches that are harder. ...
written 4.6 years ago by earonesty220
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Combining quality scores when aligning/assembling
... Suppose I have 2 reads, and I align them as a part of a joining program or an assembly: AATGCGTTTGA GCGTTAGATGCTGA Then I output one combined read: AATGCGTTTGATGCTGA How do  I combine the associated (phred scaled) quality scores in the overlapped region? If the two bases match, and say one ...
assembly quality sequence phred alignment written 4.6 years ago by earonesty220
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Comment: C: rtPCR Validated Fusion - How did it happen?
... Well, I though a bioinformatic method might be applicable, looking at the RNA Seq data we already have.   Maybe injecting an artificial sequence into the reference and looking at the pileup?  But from the comments below and other talks other PI's, we think a wet-lab experiment, involving sequencing ...
written 4.6 years ago by earonesty220
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Comment: C: rtPCR Validated Fusion - How did it happen?
... Thanks!   Looking into an inversion possibility now.  Yeah, we ruled out a read-through.   I suspect these larger chromosomal rearrangements, leaving copy-number and variation intact, are more common than we think.   Gonna play with our PacBio machine to see if we can detect it. ...
written 4.6 years ago by earonesty220
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(Closed) rtPCR Validated Fusion - How did it happen?
... I have a RNA fusion event that we confirmed with rtPCR.    The distance between the fused exons is 20 million bases, which should rule out a read-through event (correct?).   However, we don't observe unusual coverage or copy number variation in the genome. Are there other mechanisms you can think ...
fusion rna-seq written 4.6 years ago by earonesty220 • updated 4.6 years ago by mikhail.shugay3.3k
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Comment: C: Extracting regions from .bam file using a .gff or .gtf file
... http://ea-utils.googlecode.com/svn/trunk/clipper/gtf2bed ...
written 4.7 years ago by earonesty220
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Comment: C: Normalizing Rna-Seq Data Using Ercc Spike-In
... generally we've stopped using the tuxedo suite altogether for similar reasons. ...
written 4.7 years ago by earonesty220
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Comment: C: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
... They should be "comparable to expected".     In other words...you should benchmark it to an existing quality assembly.   Some k-mer duplication is, of course, expected.   What the "correct" number is varies from organism to organism.   As a rule, I would expect longer genome to have more. ...
written 4.8 years ago by earonesty220

Latest awards to earonesty

Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)

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