User: lay_0

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lay_030
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2 weeks, 4 days ago
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1 year, 4 months ago
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Posts by lay_0

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Popoolation variance-sliding.pl output shows only zero value
... Hello diva, I hope this helps, I found this comment in the popoolation wiki website "Values of 0 and na in my case came from using a bam file generated from reads using phred33 scores when the default of the Variance-sliding.pl script is to use phred64 encoding. Specify "--fastq-type sanger" to ...
written 4 weeks ago by lay_030
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Answer: A: Branch Lengths in RAxML
... I believe is number of changes per site, this is probably the same question: https://www.biostars.org/p/52359/ ...
written 5 months ago by lay_030
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Comment: C: "three genes" exemple in genoplotR
... I do have the same question and I did, in the past worked with R. I would really like to see how the "three_genes" dataset looks like, I tried several things but for some reason is not an object.... did you find your answer?... ...
written 9 months ago by lay_030
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Comment: C: something similar to FancyGene
... I did contact her, no answer yet. Thanks! ...
written 9 months ago by lay_030
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Comment: C: something similar to FancyGene
... Thanks, indeed it seems like is just maintenance problem. I did contacted the author before posting here but didn't get any answer. ...
written 9 months ago by lay_030
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something similar to FancyGene
... Hi, I used FancyGene in the past to graphically display genes and features that are close together in a sequence, and compare that genomic region between species on a scale. Well, FancyGene seems to be not working anymore, I think the person in charge has moved to a different University and the webs ...
gene structure gene clusters visualization tool written 9 months ago by lay_030 • updated 9 months ago by Michael Dondrup42k
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extract genomic sequence based on transcripts
... Hello, Can someone tell me how I can extract a full genomic sequence (intron, exons, full gene) if I have a set of transcripts and the genome in FASTA format both?. At the least the genomic coordinates for each of the genes only would work. thanks ...
genome fasta coordinates extract transcripts written 13 months ago by lay_030 • updated 13 months ago by Ram12k
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Comment: C: TMM - Normalized FPKM values for RNASeq data ?
... I have the same question as gangireddy, but how can you enter FPKMs in edgeR?, just as you would do with raw counts?, never mind the non-integers? ...
written 14 months ago by lay_030
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Comment: A: mapping initial libraries to Trinity assembly
... yes, trimmomatic output was used for the assembly. thanks, that is what I suspected....i need to repeat the RSEM. I was hoping some one would say it didn't matter. If my reads were already trimmed for adapters, and they are of really good quality before trimming... do you think is still a problem ...
written 15 months ago by lay_030
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Comment: A: mapping initial libraries to Trinity assembly
... I run trimmomatic separately, before starting Trinity, I may have missed some output there :( ...
written 15 months ago by lay_030

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Popular Question 4 months ago, created a question with more than 1,000 views. For running trimmomatic inside Trinity

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