User: Mehmet

gravatar for Mehmet
Mehmet410
Reputation:
410
Status:
Trusted
Location:
Japan
Last seen:
6 days, 11 hours ago
Joined:
3 years, 9 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 313 results • page 1 of 32 • next >
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Comment: C: Very low mapping rate of mRNA seq data
... Sorry for the late reply. I would recommend you to do: 1. You can search unmapped RNA reads against to rRNA database that you can obtain from NCBI of a very close species using blast. (please check blast manual in order to use it for this purpose). For instance, download all rRNA of the closely rel ...
written 6 weeks ago by Mehmet410
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Comment: C: any tool t make plots from blast output
... I would like to show matches (query and subject) with matching starting and ending points. I did tblastn for a genome and a proteome data. and I did blastp. In two blast runs I used local database that I generated. Any graph will be nice to show those matches; dot plot of scaffolds and proteins in ...
written 6 weeks ago by Mehmet410
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any tool t make plots from blast output
... Dear All, I was wondering if there is a tool to generate plots to show blast hits or not. ...
gene genome alignment written 6 weeks ago by Mehmet410
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Comment: C: Very low mapping rate of mRNA seq data
... Addition to suggestions by ATpoint, you can check several contamination: 1. Bacteria or virus using kraken tool. 2.rRNA contamination. You can use blast as remotely to search unmapped reads against to your species data set in NCBI. 3.If you isolated your species from environmental samples, you ca ...
written 7 weeks ago by Mehmet410
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any tool to show synteny blocks between genome and protein set
... Dear all, I have run tblastn between a genome and a protein set. Now I need to show which genomic positions the protein set hits using synteny plot. Is there any tool for that? Thank you ...
genome gene alignment written 7 weeks ago by Mehmet410
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Comment: C: Phylogenetic tree from single copy core genes (metazoa proteomes)
... You mean single copy orthologs? If yes, you can use orthofinder tool https://github.com/davidemms/OrthoFinder the tool uses proteins of species (proteome files) and find single copy proteins with their gene ids, and does alignment and produce phylogenetic tree. you can easily get sequences of s ...
written 3 months ago by Mehmet410
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Comment: C: BWA or STAR for RNAseq?
... Have you checked your transcriptome assembly befogging moving mapping of RNA reads to it? ...
written 3 months ago by Mehmet410
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Comment: C: BWA or STAR for RNAseq?
... If you want to check quality of your reference, you can use several tools; For completeness check; BUSCO: it checks how many percentage your reference is completed. It uses several databases that have well annotated genes. Find best matched database in BUSCO databases, and use it. For contaminati ...
written 3 months ago by Mehmet410
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Comment: C: RATT annotation transfer tool usage.
... Please let me know where you are having problems while you are running RATT. ...
written 3 months ago by Mehmet410
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Comment: C: RATT annotation transfer tool usage.
... OK. I will do as soon as possible. ...
written 3 months ago by Mehmet410

Latest awards to Mehmet

Popular Question 29 days ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?
Popular Question 3 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 3 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: TopHat v2.1.1- Warning: TopHat did not find any junctions in GTF file
Popular Question 4 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 4 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 5 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 5 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 5 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 5 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Popular Question 5 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 7 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 7 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 7 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Popular Question 8 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
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Popular Question 14 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
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