User: jomaco

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jomaco180
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European Union
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1 year, 4 months ago
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4 years, 11 months ago
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Posts by jomaco

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Repeatmodeler Error (Error Index Out Of Bounds!)
... Hi Dave. Not sure if this problem is properly resolved, but given the time it takes run RepeatModeler (only to find out it hasn't worked) my eventual solution was just to run ~30 duplicate jobs at the same time, and some of them worked. ...
written 17 months ago by jomaco180
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Ks calculation discrepancy (yn00 PAML, MEGA6 nei gojobori)
... The average Ks value calculated for my set of sequences using MEGA6 (Modified Nei-Gojobori (NG96) method with Jukes Cantor correction) was 0.767. The yn00 result from PAML however works out at 1.56 The results are really quite disparate - what is the reason for this difference, and is this normal? ...
ks yn00 paml mega6 nei gojobori written 17 months ago by jomaco180
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Genome coverage with pool of individuals
... If I have: - Pooled DNA from multiple different but genetically related (sibling) individuals, sequenced in one sequencing run - DNA from another individual (genetically related (sibling) to those in the pool), sequenced on its own Then If I assemble the single individual and map the pooled dat ...
genome coverage pool written 17 months ago by jomaco180
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Samtools genotype call for pool of progeny
... I have short sequencing reads from a pool of 30 progeny from two diploid parents, in the progeny at any particular site I am expecting to see either: - Two alleles (suggesting at least some of the progeny are heterozygous) Or: - One allele (suggesting all progeny are homozygous at this site) ...
snp sequencing written 18 months ago by jomaco180
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Higher coverage when using genomic sequencing reads from a pool of individuals
... Hi I have two plants, A and B (of the same diploid species). I carried out a cross A x B, and ended up with progeny C. I then mapped genomic sequencing reads (100bp) from a pool of DNA from 30 "C" progeny to plant B. I also aligned genomic sequencing reads from plant A to plant B. When I look a ...
pool genomic dna individual written 2.1 years ago by jomaco180
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Answer: A: How to align a protein set to a genome?
... If you wish to align those proteins to a reference assembly you could use the exonerate (http://www.ebi.ac.uk/~guy/exonerate/) protein2genome model which models introns. I used this when I wanted to align proteins from the TAIR10 database to our reference genome. You would also probably want to spli ...
written 2.1 years ago by jomaco180
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Statistical method of deducing the probability of a ratio being 1:2 for pairs of numbers (read depth) in a set
... By looking at the numbers below (average depth of DNA sequencing read coverage across transcript regions) I am trying to decide whether for each line V1 and V2 are equal or whether V1 is half of V2 i.e. it looks like the first 12 lines potentially have a ratio of 1:2 (V1:V2) and the rest probably ha ...
sequencing depth ratio significance written 2.2 years ago by jomaco180 • updated 2.2 years ago by Brian Bushnell15k
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Cufflinks - novel genes when using GFF file
... Hi,   When using the -G option in TopHat/Cufflinks, the manual states that the "Output will include all reference transcripts as well as any novel genes and isoforms that are assembled."  Where can I see these novel genes or the expression data for them? They don't seem to be reported... Do I ne ...
cufflinks novel genes rna-seq written 2.3 years ago by jomaco180 • updated 2.3 years ago by cpad01124.1k
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Comment: C: Cuffdiff secondary alignments (lower counts?)
... Thanks, that makes sense, which alternative tool would you recommend if that is the case (and why - presumably something to with it not being de novo)?  ...
written 2.6 years ago by jomaco180
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Comment: C: How do denovo genome/transcriptome assemblers treat ambiguous bases?
... Hi, when looking at an Abyss assembly there are lots of cases where there is a long run of a single base, where I presume N's should be, so I assumed Abyss replaced N's with a random base. Could you explain what is meant by "Replace N's based on consensus sequences that fill that base, consensus seq ...
written 2.6 years ago by jomaco180

Latest awards to jomaco

Popular Question 22 months ago, created a question with more than 1,000 views. For [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Popular Question 22 months ago, created a question with more than 1,000 views. For Deseq - Should I Include Only The Samples Being Compared?
Student 22 months ago, asked a question with at least 3 up-votes. For Deseq - Should I Include Only The Samples Being Compared?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Popular Question 2.1 years ago, created a question with more than 1,000 views. For [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Which Genome Synteny Program?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Which Genome Synteny Program?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For GO term enrichment
Supporter 2.8 years ago, voted at least 25 times.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Deseq2 Pairwise Comparison Between Conditions
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Deseq2 Pairwise Comparison Between Conditions
Student 4.3 years ago, asked a question with at least 3 up-votes. For Deseq - Should I Include Only The Samples Being Compared?

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