User: JstRoRR

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JstRoRR60
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Germany
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2 years ago
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Posts by JstRoRR

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Genome size estimation using jellyfish
... Are you calculating it manually? have you tried this online tool http://qb.cshl.edu/genomescope/ It gives you a model based genome unique length estimation. ...
written 2.2 years ago by JstRoRR60
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Answer: A: Any methods available to do QC analysis of Pacbio raw data??
... I think stsPlot is an R package dedicated for this purpose only. It plots primary analysis quality control metrics. https://github.com/PacificBiosciences/stsPlots ...
written 2.2 years ago by JstRoRR60
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Comment: C: Genome size estimation using jellyfish
... For the genome size estimation using K-mers, you have to consider all the distinct kmers. So in your case you should also consider the heterozygous peak. The heterozygous peak adds up a large part because it gives you exactly double the amount of distinct kmers with exactly half the coverage. I thi ...
written 2.2 years ago by JstRoRR60
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Comment: C: Test of selection for gene variants with in a species
... Hi Emily, thanks for your comment. Don't you think sample size would be an issue here, as we just have 8 variants. I have read about McDonald–Kreitman test, can that be of any use here? ...
written 2.2 years ago by JstRoRR60
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Test of selection for gene variants with in a species
... I have 8 gene variants from an insect species. Among these variants some are susceptible to a treatment and some are resistant. The variants are complete coding cDNA sequenced from 8 field strains. Considerable genetic variation was observed at the nucleotide level with a total of 114 polymorphic si ...
gene dn/ds ka/ks selection snp written 2.2 years ago by JstRoRR60 • updated 2.2 years ago by Emily_Ensembl20k
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Comment: C: does Illumina read length affects PacBio error correction??
... Hi WouterDeCoster, thanks for your comment. I agree that good coverage is absolutely essential but then I came across this plos paper (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046679) where authors have suggested a term SCD (short read covered depth) that defines long reads ...
written 3.2 years ago by JstRoRR60
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does Illumina read length affects PacBio error correction??
... Hi, We have a set of Illumina 250 and 100 PE sequenced eukaryotic insect clones. Now we want to further sequence some of the clones using Pacbio with 15-20X coverage. My question is which clone should I choose for PacBio sequencing? the one which was sequenced using 100 bp PE or the one with 250 bp ...
assembly readlengths pacbio illumina written 3.2 years ago by JstRoRR60 • updated 3.2 years ago by WouterDeCoster42k
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Comment: C: N50 reduces after scaffolding
... Thanks apelin20. I will try what you suggested. ...
written 3.5 years ago by JstRoRR60
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N50 reduces after scaffolding
... Hi, I have a weird situation. I am trying to scaffold a genome assembly using few Illumina mate pair libraries. The original assembly scaffold N50 is 303KB but after scaffolding using SSPACE the N50 reduces close to 160KB. I dont understand why this is happening? What confuses me is that with every ...
sspace discovar scaffolding genome assembly written 3.6 years ago by JstRoRR60 • updated 3.5 years ago by krsahlin60
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Answer: A: bcftools consensus: include the OVERHANG
... Is there any way, by using samtools/bcftools or programmatically, to retrieve softclipped bases along with consensus instead of using an assembler?? Any ideas? ...
written 3.7 years ago by JstRoRR60

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For What are SNP effects? in terms of SNPeff output file
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Things to do with the clustered groups of proteins from orthoMCL tool???

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