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List of np-hard problems in biology/bioinformatics

problem algorithm np-hard written 3.3 years ago by 11cwicks • 90 • updated 11 days ago by cmdcolin • 640

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Recent Replies

C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov by rbronste • 120
Thank you for clarification. If using just dedupe is there a way to specify that its a NextSeq ...
C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov by Brian Bushnell ♦ 13k
If you ever set the "dupedist" flag, it automatically goes into optical-only mode. To remove all...
C: Will random hexamer priming introduce SNP / SNV detection bias? by CY • 30
You are right. A second thought of this bias: This will not cause bias in SNP / SNV calling right...
C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov by rbronste • 120
I managed to get it working with the flag: -Xmx24g One other question if I am invoking the ...
C: smallRNA low percentage of mapping, N at the beninning of the reads and kmers by genomax ♦ 31k
small RNA data analysis requires pre-processing of the data in specific ways (based on the kit us...
C: correlation between genes by krushnach80 • 150
I use corrplot often but my question was would it be enough to make a correlation to show which g...
A: smallRNA low percentage of mapping, N at the beninning of the reads and kmers by Brian Bushnell ♦ 13k
You should trim leading/trailing Ns; they never help alignment, and are particularly bad with Bow...
C: Aligning protein sequences to local RNA-seq data by genomax ♦ 31k
You should do the alignments the other way around. Use the reads to map against protein DB. [DIAM...
C: Eukaryotic Genome Annotation in 2016 by Eric Normandeau ♦ 9.4k
I ended up developing a simpler genome annotation pipeline based on suggestions from a colleague....
A: Simplest genome protein annotation pipeline possible by Eric Normandeau ♦ 9.4k
I ended up developing a genome annotation pipeline based on suggestions from a colleague. You can...
C: find genes name of a specific location by h.mon ♦ 7.5k
What have you tried so far? Any error messages?
C: SNPEFF for de novo transcriptome annotation by moushengxu • 220
Well said! :) After returning the borrowed reference, make your own annotated genome the refere...

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