User: Mehmet

gravatar for Mehmet
Mehmet440
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440
Status:
Trusted
Location:
Japan
Last seen:
13 hours ago
Joined:
4 years ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 316 results • page 1 of 32 • next >
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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 4 days ago by Mehmet440
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Comment: 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 4 days ago by Mehmet440
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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 29 days ago by Mehmet440
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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 3 months ago by Mehmet440
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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 3 months ago by Mehmet440
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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 3 months ago by Mehmet440
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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 4 months ago by Mehmet440
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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 4 months ago by Mehmet440
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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 months ago by Mehmet440
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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 5 months ago by Mehmet440

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 23 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 7 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 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 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 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 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 single copy genes for phylogenetic tree after orthomcl tool
Teacher 6 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 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 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
Popular Question 8 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 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 10 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Popular Question 11 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 16 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL

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