User: Mehmet

gravatar for Mehmet
Mehmet500
Reputation:
500
Status:
Trusted
Location:
Japan
Last seen:
9 hours ago
Joined:
5 years, 1 month ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 330 results • page 1 of 33 • next >
2
votes
1
answer
115
views
1
answer
SNP data analysis from vcf file to statistical tests.
... Dear all, I have a vcf file from GATK tool. The file has 48 population of a species with scaffolds (50 scaffolds) from different locations and host species. What I need to do is to perform statistical tests and some analysis between populations. As some tests ( Fst, Tajima’s D etc.) are mostly used ...
genome next-gen snp written 4 weeks ago by Mehmet500 • updated 4 weeks ago by Kevin Blighe54k
0
votes
0
answers
118
views
0
answers
Comment: C: coverage per gene in mapped reads to genome
... starting and ending region. ...
written 3 months ago by Mehmet500
0
votes
0
answers
118
views
0
answers
Comment: C: coverage per gene in mapped reads to genome
... OK. Sorry I forgot. Below an example of read count of each gene in one sample generated by htseq. For coverage I want to have something like that. Coverage per gene in a sample. GeneName Count SpeciesA_0000000100.1 3 SpeciesA_0000000200.1 0 ...
written 3 months ago by Mehmet500
0
votes
0
answers
118
views
0
answers
Comment: C: coverage per gene in mapped reads to genome
... OK. I want coverage of each gene in each bam file (each sample ) that were produced by mapping of DNA reads to the reference genome of the same species. ...
written 3 months ago by Mehmet500
0
votes
1
answer
132
views
1
answers
Comment: C: Tophat2 RNA seq mapping
... If you want to do RNA reads mapping to your reference genome, please use hisat2 tool. ...
written 3 months ago by Mehmet500
0
votes
0
answers
118
views
0
answers
coverage per gene in mapped reads to genome
... Dear All, I have mapped reads of several samples to genome for SNP calling and now I would like to calculate coverage of each gene in each sample (reads) output (bam files). I have checked bedtools, samtools and GATK with -T DepthOfCoverage option by providing a set of gene names, but none of them ...
genome gene alignment snp written 3 months ago by Mehmet500
0
votes
1
answer
303
views
1
answers
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 5 months ago by Mehmet500
1
vote
0
answers
250
views
0
answers
Comment: C: Eukaryotic gene annotation on gene predictions
... You can use Blast2GO for annotation. ...
written 5 months ago by Mehmet500
0
votes
0
answers
882
views
0
answers
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 5 months ago by Mehmet500
0
votes
4
answers
3.2k
views
4
answers
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 7 months ago by Mehmet500

Latest awards to Mehmet

Popular Question 25 days ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 28 days ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Popular Question 11 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 4 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
Great Question 4 months ago, created a question with more than 5,000 views. For How to cluster genes in heatmap
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 Phylogeny based on multiple sequences
Great Question 4 months ago, created a question with more than 5,000 views. For Heatmap based with FPKM values
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 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 Phylogeny based on multiple sequences
Popular Question 8 months ago, created a question with more than 1,000 views. For Phylogeny based on multiple sequences
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?
Teacher 8 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 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 10 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 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2094 users visited in the last hour