User: Mehmet

gravatar for Mehmet
Mehmet300
Reputation:
300
Status:
Trusted
Location:
Japan
Last seen:
6 hours ago
Joined:
3 years, 3 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 270 results • page 1 of 27 • next >
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Comment: C: Kraken Build Custom Database
... It takes usually, maybe mostly, longggg time, and 128 GB and 1 TB will not be sufficient based on my experience. Instead of that, you can use standard kraken database. ...
written 4 days ago by Mehmet300
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Comment: C: Help with finding gene families in genome
... If you have a gene file (amino acid sequences) from your genome and you want to know which gene families your genes belong to, You can use: 1. Pfam website; (you need to split your gene file into small files) http://pfam.xfam.org/search#tabview=tab1 2. you can use hmmer that also uses Pfam datab ...
written 11 days ago by Mehmet300
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Comment: C: Masking repeats in fungal genomes
... You mean masking during annotation? Why do you do this? In annotation, you will try to find function of genes, so you already have gene sequences. But in genome there are genes and other non-coding sequences in which you need to find repeats. To me, you can mask genome. Because in annotation you kno ...
written 11 days ago by Mehmet300
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Comment: C: RNAseq data with no replicates.What novel or different analysis can be done??
... First, do a deep search on the literature to see which disease or pathological agent the plant species is used as a drug. Try to find immunological proteins of the plant species, and depending on the drug, you can search motifs of candidate proteins that are associated with "binding function". Compa ...
written 11 days ago by Mehmet300
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Comment: C: RNAseq data with no replicates.What novel or different analysis can be done??
... It depends on what you want to find. You can perform differential gene expression analysis if you have two different transcriptome assembly (you can use the tool gfold). For more analyses, you can focus on biology of the plant species and therefore you can do more deep analyses depending on biology, ...
written 11 days ago by Mehmet300
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Comment: C: Masking repeats in fungal genomes
... You can do masking before annotation. Masking can be useful to see repeat elements and their length in genome to get some stats about the genome. ...
written 11 days ago by Mehmet300
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Comment: A: orthoMCLInstallSchema error : cant form a databse
... Alternatively, you can use orthofinder if you can not have access. ...
written 15 days ago by Mehmet300
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Comment: C: Genome Annotation, specific pipeline
... Hi, Please provide more information about what you want to do. For example, what do you mean by re-annotate ? Do you have a already annotated genome ? and you want to annotate again? I guess you made a newer genome assembly and you want to annotate again? if so, you can do annotation transfer (you ...
written 5 weeks ago by Mehmet300
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Comment: C: How to cluster genes in heatmap
... Hi Kevin, I was able to show FPKM box plot of rows (genes) and columns (samples/conditions) in the heatmap without annotation. ...
written 6 weeks ago by Mehmet300
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Comment: C: How to cluster genes in heatmap
... Hi Kevin, I was able to produce annotated box plot based on FPKM values in the heatmap. I mean this is the command that I added to Heatmap function and it put FPKM values in cell in the heatmap: cell_fun = function(j, i, x, y, width, height, fill) {grid.text(sprintf("%.1f", shorteffec.fpkm. ...
written 7 weeks ago by Mehmet300

Latest awards to Mehmet

Popular Question 8 days ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 12 days ago, created a question with more than 1,000 views. For single copy genes for phylogenetic tree after orthomcl tool
Popular Question 26 days ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Popular Question 8 weeks ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
Supporter 5 months ago, voted at least 25 times.
Popular Question 7 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 LASTZ aligner for HaploMerger
Popular Question 16 months ago, created a question with more than 1,000 views. For Trinity de novo transcript assembly too many transcripts
Centurion 18 months ago, created 100 posts.
Popular Question 20 months ago, created a question with more than 1,000 views. For CEGMA report meaning
Popular Question 20 months ago, created a question with more than 1,000 views. For Augustus training and artemis
Popular Question 22 months ago, created a question with more than 1,000 views. For CEGMA report meaning

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