User: lay_0

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lay_050
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Posts by lay_0

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Easy way to run easily orthoMCL (Copy & paste)
... Thanks a lot!, I could spot the error by looking at the SimilarSequences.txt files, I had a wrong header ( several limes of "processing XX genome" just before the columns start). That was because I used nohup to redirect output. Now my SimilarSequences head table looks like: Atra|XP_013197910.1 ...
written 5 months ago by lay_050
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Answer: A: Easy way to run easily orthoMCL (Copy & paste)
... Hi, thanks for posting the streamlined help. I was able to run everything up to step 8 and then, after submitting my command for step 9 I got the following error: DBD::mysql::st execute failed: Row 1 doesn't contain data for all columns at /usr/local/bin/orthomclLoadBlast line 39, line 13. I ...
written 5 months ago by lay_050 • updated 5 months ago by RamRS22k
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Comment: A: Does the PacBio Reads only contain positive (+) strand?
... Did you get a concrete answer for your question?. I am wondering the same thing, I believe all the Isoforms are in the positive strand ... ...
written 17 months ago by lay_050
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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 23 months ago by lay_050
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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 2.2 years ago by lay_050
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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 2.6 years ago by lay_050
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Comment: C: something similar to FancyGene
... I did contact her, no answer yet. Thanks! ...
written 2.6 years ago by lay_050
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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 2.6 years ago by lay_050
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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 2.6 years ago by lay_050 • updated 2.6 years ago by Michael Dondrup46k
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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 3.0 years ago by lay_050 • updated 3.0 years ago by RamRS22k

Latest awards to lay_0

Popular Question 6 months ago, created a question with more than 1,000 views. For something similar to FancyGene
Popular Question 17 months ago, created a question with more than 1,000 views. For Getting full protein names from Uniprot-Swissprot identifiers or short names
Popular Question 2.2 years ago, created a question with more than 1,000 views. For running trimmomatic inside Trinity

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