Moderator: lh3

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lh330k
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Posts by lh3

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Comment: C: Stranger Things: unexpected limitations of popular tools
... I can understand why you say yours is a paradigm shift: optional columns unify multiple formats, but optional tags don't. If you had implemented this 20 years ago and a toolbox working with it as efficiently as other unix tools, your proposal might have greatly influenced bio format design – I can't ...
written 11 months ago by lh330k
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Comment: C: Stranger Things: unexpected limitations of popular tools
... My understanding is that to an alignment format, you still propose to have fixed columns and optional columns. The major difference from SAM would be that each line ought to have a fixed number of optional columns, as are defined in the header. This could work, but I am not sure how much it improves ...
written 11 months ago by lh330k
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Comment: C: Stranger Things: unexpected limitations of popular tools
... I always think the biggest mistake in SAM (not BAM) is the integer flag because it is not human readable. I proposed letter flags, using one letter for one flag bit, but the proposal fell through. Probably I should have acted more firmly at the time. On the other hand, I am not sure how binary flag ...
written 11 months ago by lh330k
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Answer: A: Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver
... Canu uses alignments between pacbio reads to correct away most sequencing errors in raw reads. You can't do much better without using the signal information. To achieve high-quality consensus, Quiver is your only choice. ...
written 12 months ago by lh330k
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Comment: C: Where and how NGS techniques are heading for the next 5 years?
... Another major problem with the current long-read technologies is that they are unable to call SNPs from diploid genomes. In theory, PacBio probably can achieve the goal, but no available tools match the accuracy of Illumina data yet. Nanopore can't so far, even in theory. Without solving this proble ...
written 12 months ago by lh330k
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Answer: A: confusion in the DeBruijn Graph
... On the other bioinfo Q&A, one of the best questions is about [the difference between mathematical and bioinformatics de Bruijn graphs](https://bioinformatics.stackexchange.com/questions/146/how-to-make-a-distinction-between-the-classical-de-bruijn-graph-and-the-one-de). That question made me thi ...
written 12 months ago by lh330k
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Comment: C: Are these false somatic variants? Visual inspection with IGV
... 29 is pretty low. A blat score 300 is high enough to make me worry. What is coordinate of this region? The genome build? ...
written 13 months ago by lh330k
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Comment: C: Are these false somatic variants? Visual inspection with IGV
... In somatic mutation calling, multiple SNVs on one read are mostly false positives even if you see no evidence in the paired normal. I am not sure what is the exact cause, but most SNVs like these don't get validated experimentally. ...
written 13 months ago by lh330k
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Comment: C: Selecting Random Pairs From Fastq?
... Yes, as long as you use the same -s. ...
written 13 months ago by lh330k
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Comment: C: Variant annotation and filtration server ALAPY Genome Explorer (AGx)
... Most biologists don't run VM, let alone install a Linux in it. Your tool should simplify data processing, not complicate it. I don't know what industrial users will think about the tool, but I am moderately certain that few academia users will use it. The dependencies you chose are too heavy. I don ...
written 13 months ago by lh330k

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