User: Mehmet

gravatar for Mehmet
Mehmet470
Reputation:
470
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Trusted
Location:
Japan
Last seen:
1 week ago
Joined:
4 years, 6 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 4 months ago by Mehmet470
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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 4 months ago by Mehmet470
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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 4 months ago by Mehmet470 • updated 4 months ago by h.mon26k
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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 5 months ago by Mehmet470
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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 6 months ago by Mehmet470
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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 6 months ago by Mehmet470
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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 7 months ago by Mehmet470
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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 9 months ago by Mehmet470
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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 9 months ago by Mehmet470
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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 9 months ago by Mehmet470

Latest awards to Mehmet

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 6 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 6 weeks ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Teacher 6 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 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 single copy genes for phylogenetic tree after orthomcl tool
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 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 No one knows how to get single copy orthologs from orthomcl output?
Popular Question 6 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 8 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 8 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 9 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 11 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 11 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 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 single copy genes for phylogenetic tree after orthomcl tool
Teacher 12 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 12 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 13 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool

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