User: Mehmet

gravatar for Mehmet
Mehmet490
Reputation:
490
Status:
Trusted
Location:
Japan
Last seen:
4 weeks, 1 day ago
Joined:
4 years, 9 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 324 results • page 1 of 33 • next >
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Comment: C: Finding orthologs in a organism with a genome duplication.
... You can use OrthoFinder, which will give you one-to-one, one-to-many, many-to-one, and many-to-many. ...
written 8 weeks ago by Mehmet490
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Comment: C: Eukaryotic gene annotation on gene predictions
... You can use Blast2GO for annotation. ...
written 8 weeks ago by Mehmet490
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Comment: C: RATT annotation transfer tool usage.
... Hi Peri, Sorry for my late reply. Can you try this? ./start.ratt.sh embl_files_directory/ New.genome.fa old2new Assembly ...
written 10 weeks ago by Mehmet490
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Comment: C: Augustus training and artemis
... Hi, Can you please write what command you have used? and Did you check seq names in fasta file? The seq names should be same in the gff file? what option did you use in your command? /scripts/gff2gbSmallDNA.pl gff-file seq-file max-size-of-gene-flanking-DNA output-file [options] here is my ...
written 3 months ago by Mehmet490
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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 7 months ago by Mehmet490
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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 7 months ago by Mehmet490
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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 7 months ago by Mehmet490 • updated 7 months ago by h.mon28k
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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 9 months ago by Mehmet490
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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 9 months ago by Mehmet490
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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 9 months ago by Mehmet490

Latest awards to Mehmet

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 5 weeks ago, created a question with more than 5,000 views. For Heatmap based with FPKM values
Popular Question 3 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 3 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
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 5 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
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 5 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Teacher 5 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 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 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 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 8 months ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 10 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 10 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 12 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 12 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 13 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 14 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 15 months ago, created a question with more than 1,000 views. For No one knows how to get single copy orthologs from orthomcl output?

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