User: Mehmet

gravatar for Mehmet
Mehmet460
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460
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Trusted
Location:
Japan
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an hour ago
Joined:
4 years, 2 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 320 results • page 1 of 32 • next >
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Comment: C: visualize amino acid changes in genes that are positively selected after codeml
... Thank you for your suggestions. I mean I want to show where amino acid changes of a protein occurred due to positive selection. ...
written 1 hour ago by Mehmet460
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Comment: C: Low Mapping percentage with Minimap2 due to contamination
... you can try Kraken [https://ccb.jhu.edu/software/kraken/][1] [1]: https://ccb.jhu.edu/software/kraken/ ...
written 8 hours ago by Mehmet460
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visualize amino acid changes in genes that are positively selected after codeml run
... Dear All, can anyone suggest a tool/software to visualize amino acid changes of positively selected genes? I have run codeml and detected positively selected genes, and now I want to produce 3D graphs of genes by emphasizing amino acid changes. Do you know any tool or software for this? ...
gene genome alignment written 9 hours ago by Mehmet460 • updated 7 hours ago by h.mon24k
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Comment: C: RATT annotation transfer tool usage.
... Sorry for being late. Could you please let me know at which point you need help? At least I can do this until I complete tutorial. ...
written 6 weeks ago by Mehmet460
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Comment: C: Problem in running STAR
... 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) These are mostly memory error. You should increase available memory for STAR. ...
written 8 weeks ago by Mehmet460
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Answer: C: Bowtie2 mapped just 50% of the reads
... If you do aligment of RNAs to genome of an eukaryotic organism, C. elegans in this case, you should use splicer aligner. STAR is a splicer aligner, meaning needs exon-intron boundaries to align RNA reads to genome. Hisat2 is another one. You should use splicer aligner for this reason. This is why ...
written 8 weeks ago by Mehmet460
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Comment: C: What does ab initio mean?
... In addition to h.mon`s comment when there is no reference set (genome assembly, gene annotation information) it refers to "ab initio", meaning you need to produce for the first time. ...
written 12 weeks ago by Mehmet460
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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 5 months ago by Mehmet460
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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 5 months ago by Mehmet460
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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 5 months ago by Mehmet460

Latest awards to Mehmet

Popular Question 14 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 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 29 days ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 10 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 11 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 No one knows how to get single copy orthologs from orthomcl output?
Popular Question 4 months 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 4 months 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 months 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 7 months 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 7 months 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 7 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 8 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Teacher 8 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 8 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 9 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 9 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 9 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 9 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 9 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Popular Question 10 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 11 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 11 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 12 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Popular Question 13 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL

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