User: ricardoguerreiro2121

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Germany
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Posts by ricardoguerreiro2121

<prev • 27 results • page 1 of 3 • next >
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Comment: C: What are chimeric reads?
... Is there a way of forcing a linear alignment with bwa? ...
written 21 days ago by ricardoguerreiro212150
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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 22 days ago by ricardoguerreiro212150
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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 23 days ago by ricardoguerreiro212150 • updated 2 days ago by Asaf7.0k
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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 28 days ago by ricardoguerreiro212150
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Answer: A: Extracting homologous proteins from genome ( blat or exonerate)
... I think I have found my ideal answer: Run exonerate Then in Python: qresult = SearchIO.parse("exonerate_outfile", 'exonerate-text') for i in qresult: hsp = i[0][0] print("".join(list(hsp.hit_all[0]))) ...
written 5 weeks ago by ricardoguerreiro212150
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Extracting homologous proteins from genome ( blat or exonerate)
... Hi, I would like to quickly extract proteins from various novel plant genomes, by finding homology with documented proteins (ex: A. thaliana), for the purpose of phylogenetic analysis. A recent [paper][1] works with an old tool, Blat, that does just that. But the results of blat are a table of hit ...
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Is Genome heterozygosity a problem for gene annotation?
... Quick question: How important is it to reduce uncollapsed heterozygosity in a Genome assembly before proceeding to Gene annotation? With uncollapsed heterozygosity I mean: The existence of alternative contigs (haplotigs) for one same region of the genome, for an organism that possesses multiple a ...
genome gene heterozygosity diploid annotation written 5 weeks ago by ricardoguerreiro212150 • updated 5 weeks ago by lieven.sterck6.9k
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Comment: C: gene set filter/selection for training ab initio annotation tools
... I didn't even realize this was necessary. The maker tutorials don't mention it at all, they just proceed to SNAP modelling with all genes, using only "fathom" as quality control. Does this make a very big difference in results? Where can I learn about it? Cheers, P.S: Thank you so much for sh ...
written 7 weeks ago by ricardoguerreiro212150
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Comment: C: gene set filter/selection for training ab initio annotation tools
... It's your output of maker after using: ...../src/maker/bin/gff3_merge -d your_name_master_datastore_index.log He called it evidence_based because your first maker run should be using protein and RNA (ESTs) evidence to detect genes. The next maker round you do will be without these evidences (you s ...
written 7 weeks ago by ricardoguerreiro212150
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Comment: C: Create de novo repeat library
... Great, thanks! Is the result of this as powerful as makers advanced repeat library preparation? Many of the steps are similar, but this is smaller. ...
written 9 weeks ago by ricardoguerreiro212150

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