User: Mehmet

gravatar for Mehmet
Mehmet600
Reputation:
600
Status:
Trusted
Location:
Japan
Last seen:
2 days, 1 hour ago
Joined:
5 years, 9 months ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 358 results • page 1 of 36 • next >
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Comment: C: RNASeq, gtf file
... [https://www.biostars.org/p/453264/#454147][1] [1]: https://www.biostars.org/p/453264/#454147 ...
written 9 weeks ago by Mehmet600
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Comment: C: Freebayes error message
... how many memory did you use? Mostly, core dumped error points lack of enough memory. Another possible reason for this error could be interrupted files. you may try to increase memory and check your bam files. ...
written 9 weeks ago by Mehmet600
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Comment: C: GO for novel species
... Have you checked Blast2GO for GO analysis? You can give DNA or protein sequences of your novel species as input to Blast2GO. Blast2Go uses multiple sources (interpro, PFAM etc) and map to GO term also gives PFAM ids for PFAM domain and description. Using GO given by Blast2GO you can perform GO enric ...
written 10 weeks ago by Mehmet600
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Comment: C: filtered tab delinited file with awk
... I guess FPKM is the 13th column. if so, you can print transcripts that have FPKM values greater than 0.5 as below. cat yourfile | awk '{if($13>=0.5) print}' > output ...
written 12 weeks ago by Mehmet600
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Comment: C: Best method for phylogeny on bacterial genes
... I can recommend: 1. To concatenate all alignments (40 alignments) into a super matrix then to use the super matrix as input for a phylogenetic tool. 2. You can generate 40 separate trees and later you can make a final consensus tree. (IQ-TREE has an option for this) Importantly, There may be lo ...
written 12 weeks ago by Mehmet600
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Comment: C: tree with selected species
... For phylogeny there are many tools. some of them are : RAxML IQ-TREE2 PAUP Phylobayes MrBayes for divergence time analyses (million years as you wrote) you can youse BEAST tool as @Joe said, but you need to know molecular clocks. For this you can read manuscripts and can have an idea about molecula ...
written 12 weeks ago by Mehmet600
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Comment: C: Eukaryotic Genome Annotation for a non-model organism
... What is your aim? What kind of additional data you have and/or you can have? Depending on your aim you can determine which analyses are needed. ...
written 3 months ago by Mehmet600
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Comment: C: R: How to parse taxa from one row to multiple columns?
... A linux solution: cat yourfile |sed 's/D....//g' | sed 's/;/" "/g'| sed 's/_.*//g' | sed 's/"$//g' output is "Archaea" "Asgardaeota" "Lokiarchaeia" ...
written 3 months ago by Mehmet600
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Comment: C: Is it possible to remove unwanted tissue contamination in transcriptome analysis
... you are right, it clearly is seen that distribution of samples are not correlated well. (14 weeks and 8.5 weeks named samples especially). Is it possible to mislabeling some samples (14 weeks and 8.5 weeks?). I would do clustering of DEG genes to separate them and assign to brain and muscular usin ...
written 3 months ago by Mehmet600
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Comment: C: Is it possible to remove unwanted tissue contamination in transcriptome analysis
... how did you know that brain transcriptome was contaminated by muscular tissue? Based on GO and expression levels? Or during data preparation for analysis? Have you done PCA or MDS for your samples to see correlation of samples? ...
written 3 months ago by Mehmet600

Latest awards to Mehmet

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 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 9 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?
Student 11 weeks ago, asked a question with at least 3 up-votes. For Heatmap based with FPKM values
Scholar 3 months ago, created an answer that has been accepted. For A: Eucaryotic gene predictor within eucaryote genome
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 Phylogeny based on multiple sequences
Popular Question 6 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
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 Phylogeny based on multiple sequences
Voter 6 months ago, voted more than 100 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 7 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 7 months ago, created a question with more than 5,000 views. For How to cluster genes in heatmap
Popular Question 9 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 9 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 9 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 10 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
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 Phylogeny based on multiple sequences
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 Phylogeny based on multiple sequences
Great Question 12 months ago, created a question with more than 5,000 views. For How to cluster genes in heatmap

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