User: Chvatil

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Chvatil50
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Posts by Chvatil

<prev • 152 results • page 1 of 16 • next >
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Find repeat regions on 100 eukaryotic assemblies
... Hello everyone, I have a hundred genomes and I'm looking for `repeated regions` along these `assemblies`. First of all, I thought of using `RepeatModeler`, only the most familiar among you know that it is not at all optimized software that requires a lot of resources and calculation time, which is ...
assembly repeat written 4 weeks ago by Chvatil50 • updated 4 weeks ago by colindaven2.5k
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Comment: C: Question about codeml
... Well I'm interested in making a distribution of dS along branches, so for instance I want to take two species in the tree and say: ok the sum of dS (kind of divergence time) between those two species is 3.4, and by adding 300 gens I want to say : ok the dS value between species 1 and 2 is comprised ...
written 5 weeks ago by Chvatil50
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Question about codeml
... Hello everyone, I need for a project to calculate `dS along branches` for `300 house keeping genes` within a phylogeny of `100 species`. The idea is to get a dN/dS distribution of dS for them. But here is my question, do you think it is better to : - Build a phylogeny for each house keeping ge ...
phylogeny tree paml ds codeml written 5 weeks ago by Chvatil50
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Comment: C: RepeatModeler : build_lmer_table failed. Exit code 256
... Yes when I run the ```/beegfs/data/TOOLS/RepeatScout-1.0.6/build_lmer_table``` I get the same output as you . Well I sue 80 RAM it should be enought no? The thing weird is that when I run this localy it works but on the cluster of my labs it does not ...
written 7 weeks ago by Chvatil50
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Runmode = -2 in Biopython PAML impossible ?
... The question is in the title, I want to calculate dN/dS between two sequences using PAML implemented in biopython but I get this error message : cml = codeml.Codeml() cml.alignment = "/beegfs/data/Species_phylogeny/Busco_DNA_seqs_pairs/"+new_pair_name+".fa" cml.out_file = "/beegfs/dat ...
python3 paml codeml biopython written 7 weeks ago by Chvatil50
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Comment: C: Plot information stored in dataframe within a tree (ggtree)
... thanks, but I also need to keep bootstrap values (they are not shown here but they will appear as well in the figure) ...
written 8 weeks ago by Chvatil50
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Programme to calculate dN/dS between pair of sequences in a seq alignment
... Hello everyone, I'm writing this post because I wanted to know if any of you know of an efficient software that takes a sequence codon alignment as input, and calculates the `dN/dS` between each `pair of sequence` ? The only constraint is that I'm looking for a maximum **lihelihood** and/or **Baye ...
gene dn/ds sequence paml codeml written 8 weeks ago by Chvatil50
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Extract specific variant genome ID from a VCF file
... Hello I have a specific variant file (vcf) dowload from ftp:/­/­ftp.­1000genomes.­ebi.­ac.­uk/­vol1/­ftp/­data_collections/­1000_genomes_project/­release/­20190312_biallelic_SNV_and_INDEL/­ALL.­chr9.­shapeit2_integrated_snvindels_v2a_27022019.­GRCh38.­phased.­vcf.­gz.­tbi so I get a file ca ...
genome vcf variant written 12 weeks ago by Chvatil50 • updated 12 weeks ago by Jorge Amigo12k
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Comment: C: Difference between mate-pair, paired-end and long read
... Thank you for this explanation, so If I'm not wrong we can use long read and mate pair in order to assemble contigs together (scaffolding) right ? I'm asking this question because wen I have assemblies made only from short paired-end, I have incorrect assembly where I see `misassembly breakpoints` a ...
written 3 months ago by Chvatil50
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Comment: C: Difference between mate-pair, paired-end and long read
... Oh sorry I did not know that, someone gave me an answer then I cannot delete it now.. ...
written 3 months ago by Chvatil50

Latest awards to Chvatil

Popular Question 5 months ago, created a question with more than 1,000 views. For Get summary of augustus ouput (gff)
Supporter 6 months ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For Issue using MaSuRCA-3.2.6
Popular Question 9 months ago, created a question with more than 1,000 views. For compare 2 dataframe with pandas
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Popular Question 19 months ago, created a question with more than 1,000 views. For Cannot install NumPy using pip and import it
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Epic Question 19 months ago, created a question with more than 10,000 views. For C extension: No module named 'pandas._libs.tslib' not built (pandas)
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