User: Plantae

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Plantae380
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Posts by Plantae

<prev • 31 results • page 1 of 4 • next >
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Standalone Gc Correction Tools
... hi, all, i try to find CNVs from a high-depth resequenced sample (>30x), which is a plant species. however, several CNV detect tools could only be used for human genomes, i am wondering if there are some standalone tools that can get gc-corrected read counts using BAM file as inputs. then we c ...
gc cnv written 5.7 years ago by Plantae380 • updated 3.6 years ago by R Ravi10
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Comment: C: Draw Diagrams For Intersection Between Many Sets
... The two figure I attached show overlaps between 10 sets, 22 sets. i think it is impossbile to draw venn diagrams for so much sets. ...
written 5.9 years ago by Plantae380
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Draw Diagrams For Intersection Between Many Sets
... Venn diagrams are often used for datas with less than 5 sets i found some figures are insteresting, but don't know how to draw figures like this: ...
written 5.9 years ago by Plantae380 • updated 5.9 years ago by quentin.delettre430
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Too Many Genes Under Positive Selection
... Our lab sequenced 7 genomes from the same organism, the divergence time between these genomes is less than 0.5 Mya. ~ 42000 ortholog gene families were constructed from these genomes, to find positive selected genes, I use codeml M2a vs M1a to test (df=2) for positive selection, using a FDR cutoff ...
paml codeml selection written 6.0 years ago by Plantae380 • updated 6.0 years ago by Rahul Sharma560
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Find Disruptions Of Gene Structures Based On Gene Sequence Aligment?
... I have two closely related genomes, with all genes annotated, Ortholog gene pairs were identified from these two genomes, now I want to find how many genes come with large effect structural variations, such as exon deletion, frameshift, premature codons etc. I have aligned all ortholog gene pairs ...
variation alignment genomics structural written 6.2 years ago by Plantae380 • updated 6.2 years ago by Josh Herr5.6k
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Comment: C: Calculate Average Dn And Ds For Gene Families
... codeml reports DN or DS in each branch on the tree, but without average estimates. One simple methods was calculate averages values by summing all branch DN or DS values, then divided by branch numbers. I also calcuated the average DN and DS using codeml's runmode "-2", then averaging the values co ...
written 6.6 years ago by Plantae380
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Calculate Average Dn And Ds For Gene Families
... hi, all I have several single-copy gene families identified from 12 genomes, Now I want to know evolution rate differences between these gene families, I got average DN/DS from PAML package: average DN/DS can be calculated through codeml 's M0 model (model=0, NSsites=0), but how to calculate avera ...
gene selection written 6.6 years ago by Plantae380 • updated 5 weeks ago by mariamcurbelo20610
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Comment: C: Extract Alignment From Very Large Bam File
... I indexed the bam file, then use your method. It is really very fast, much faster than bedtool ...
written 6.7 years ago by Plantae380
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Extract Alignment From Very Large Bam File
... I have bam files ~50Gb, which is read alignments onto a reference genome. now I want to extract some regions of alignment, but I found methods like samtools view -L region.bed all.bam is too slow, usually taken more than 2 hours (even if very small region are submit) Are there any other methods t ...
bam written 6.7 years ago by Plantae380 • updated 4.4 years ago by dariober9.9k
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Haploview Memory Issues
... I try to use Haploview to contructure LD blocks for my SNP datasets. My SNP dataset is very large, for each chromosome, ~100000 sites are present. But I could not calculate LD blocks using HAPLOVIEW, due to out of memory errors, I have set the memory usage for HAPLOVIEW to 40GB, the computing sti ...
genome haplotype ld written 6.8 years ago by Plantae380

Latest awards to Plantae

Popular Question 5.9 years ago, created a question with more than 1,000 views. For Draw Diagrams For Intersection Between Many Sets
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Extract Alignment From Very Large Bam File
Student 6.8 years ago, asked a question with at least 3 up-votes. For Analyse Population Genomics Data With Different Coverage
Student 7.0 years ago, asked a question with at least 3 up-votes. For How To Draw Genome Features Along Chromosome
Popular Question 7.0 years ago, created a question with more than 1,000 views. For How To Draw Genome Features Along Chromosome
Student 7.0 years ago, asked a question with at least 3 up-votes. For Synchronization Of Pair-End Reads
Popular Question 7.7 years ago, created a question with more than 1,000 views. For Quality Contol For Illumina Transcriptome Reads
Student 7.9 years ago, asked a question with at least 3 up-votes. For Problems For Mapping Contigs Onto Reference
Student 8.3 years ago, asked a question with at least 3 up-votes. For Genome Assembly With Physical Map

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