User: Mehmet

gravatar for Mehmet
Mehmet410
Reputation:
410
Status:
Trusted
Location:
Japan
Last seen:
2 hours ago
Joined:
3 years, 8 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 309 results • page 1 of 31 • next >
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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 20 hours 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 5 weeks 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 6 weeks 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 7 weeks 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 8 weeks ago by Mehmet410
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Comment: C: RATT annotation transfer tool usage.
... OK. I will do as soon as possible. ...
written 9 weeks ago by Mehmet410
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Answer: C: TopHat v2.1.1- Warning: TopHat did not find any junctions in GTF file
... Tophat and Hisat2 are splicer aligner, therefore there must be intron-exon junction. In bacteria, as you know, there is no intron. I suggest you use not splicer aligner; such as Bowtie2. ...
written 9 weeks ago by Mehmet410
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Comment: C: get domains of proteins
... Please have a look: [https://www.biostars.org/p/238489/][1] [1]: https://www.biostars.org/p/238489/ ...
written 9 weeks ago by Mehmet410
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Comment: C: SHAPEIT Segmentation Fault on Input Read-In
... Can you increase memory that you allocate for this program? ...
written 11 weeks ago by Mehmet410
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Comment: C: segmentation fault (core dumped) when running unikalow
... Yes, it is a kind of memory issue. ...
written 11 weeks ago by Mehmet410

Latest awards to Mehmet

Popular Question 4 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 5 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 6 weeks ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 9 weeks ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Teacher 9 weeks 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 12 weeks 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
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
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 phylogenetic tree after ortholog finding by orthoMCL
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 6 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Popular Question 7 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 12 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
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