Moderator: lh3
lh3 ♦ 31k
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Posts by lh3
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... 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 2.3 years ago by
lh3 ♦ 31k
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... 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 2.3 years ago by
lh3 ♦ 31k
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... 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 2.3 years ago by
lh3 ♦ 31k
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... 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 2.3 years ago by
lh3 ♦ 31k
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... 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 2.4 years ago by
lh3 ♦ 31k
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... 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 2.4 years ago by
lh3 ♦ 31k
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1.5k
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... 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 2.4 years ago by
lh3 ♦ 31k
2
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1
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1.5k
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... 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 2.4 years ago by
lh3 ♦ 31k
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... Yes, as long as you use the same -s. ...
written 2.4 years ago by
lh3 ♦ 31k
0
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... 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 2.4 years ago by
lh3 ♦ 31k
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