User: ricardoguerreiro2121

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Posts by ricardoguerreiro2121

<prev • 33 results • page 1 of 4 • next >
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Comment: C: MAKER annotation post processing (AED score)
... The first question has not been answered yet. I'd like knowing. I'm right now filtering on 0.5 AED score. ...
written 8 hours ago by ricardoguerreiro212160
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Answer: A: Principle Component Analysis (PCA) for GWAS (SNP genotype data)
... Hi, Did you find the answer? I think it's as simple as providing the n.PC = 10 parameter in your sommer::GWAS function. It does everything automatically. Cheers, Ricardo ...
written 11 days ago by ricardoguerreiro212160
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Comment: C: Multiple mapping with longreads - Get primary mapping
... Thank you for clearing it up. Same when I use the raw pacbio reads? I expect Structural Variation, the reference is from a different genotype of my plant. I want to see where my reads map in the reference, in order to clean out reads that don't belong to the target region that I am trying to assem ...
written 6 months ago by ricardoguerreiro212160
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Multiple mapping with longreads - Get primary mapping
... Hello, I'm mapping scaffolded pacbio to a reference assembly with Minimap2. The scaffolds are very long, so I would expect mostly unique mappings. But that is far away from the case. I get the 4x more mappings than my original reads. My questions are: - Is this normal with such long scaffolds? ...
minimap2 long reads samtools mapping pacbio written 6 months ago by ricardoguerreiro212160 • updated 6 months ago by WouterDeCoster44k
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Mapping (minimap2) nanopore reads to parent species to confirm hybridization
... Hey, I have created a scientifically interesting hybrid of two related plant species, but I am not sure if it really is hybrid, so I got low coverage nanopore sequencing for them. I have relatively good assemblies for both parents. The idea is now to map the reads of the new hybrid to each of the ...
minimap2 parents hybrids long reads written 6 months ago by ricardoguerreiro212160
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Comment: C: Creating assembly graphs .gfa
... What if I try to do an assembly using my scaffolds as reads. Wont it build an assembly graph for them? ...
written 6 months ago by ricardoguerreiro212160
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Comment: C: What are chimeric reads?
... Is there a way of forcing a linear alignment with bwa? ...
written 8 months ago by ricardoguerreiro212160
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Comment: C: Reference-guided assembly from short reads
... I would say so. Try your best assembly possible and then feed it to RaGOO with the reference. I'm trying this right now. Did you do it? How does it work for you? ...
written 8 months ago by ricardoguerreiro212160
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Creating assembly graphs .gfa
... Hello all, Is it possible to create a .gfa file out of a fasta file? This is outputted by some assembly programs and is great for assembly visualization in [bandage][1]. But I have now scaffolded my assembly and would like to visualize that as well. Cheers, Ricardo [1]: https://github ...
assembly visualization gfa graph bandage written 8 months ago by ricardoguerreiro212160 • updated 7 months ago by Asaf8.4k
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Comment: C: Trimming out primer sequences in the middle of reads
... Hello, does your script also remove the reverse complement? Do I find it within the BBmap scripts? ...
written 8 months ago by ricardoguerreiro212160

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Popular Question 4 months ago, created a question with more than 1,000 views. For Pysam VariantFile.fetch() without specifying contig
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