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Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
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Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
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langziv
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Thanks.
I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
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Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
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> so I don't think the genome size is available.
Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
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For additional information,
"Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
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langziv
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By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
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langziv
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Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929.
I just rem…
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c.
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actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
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Correct. Data that went into the assembly.
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
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langziv
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Total bases (number of reads * read length) should be calculated after removal of adapters, right?
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If I understand correctly, Blast can tell you how many results it has gotten but it can't tell you how many it is going to get, therefore i…
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I don't understand your logic. You don't know what phasing is but are confident it is not required, and your proof is that relatives were d…
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It's from Nebula genomics. It must be possible to deduce parental alleles, since I converted the VCF file into a Myheritage VCF file and th…
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bk11
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You can simply do `Idents(seurat.integrated) <- "Type"` instead of `seurat.integrated <- SetIdent(seurat.integrated, value=seurat.integrate…
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