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With this increased speed, we were able to create paralog-specific maps from the 2,500 samples from the 1000 Genomes Project. We made use of the newly sequenced 30X coverage samples made available by the NY Genome Center @nygenome @1000genomes @genome_gov
Here in 2020 it is remarkable how useful the 1000 Genomes Project remains. The freely accessible data and samples continue to be the standard for uncountable analyses of human genetic diversity.
We applied QuicK-mer2 to these sequences and report the data in an easily viewable track hub that anyone can load.https://github.com/KiddLab/kmer_1KG …
Coming back to where this thread started: when you look across thousands of samples it is not surprising that you find rare variants that were previously missed.
At the APOBEC3 locus, we observed several rare CNVs. Including what appears to be a APOBEC3B duplication, as well as apparent variation at other family members such as APOBEC3C, APOBEC3D, and APOBEC3Fpic.twitter.com/7zoOYVjXfN
Of course, this is only a copy-number estimate. The structure, sequence, and potential functional impact of this rare variation remains to be demonstrated.
There are many other interesting examples of gene parlog variation in these samples. We think QuicK-mer2 will enable the routine assessment of such differences in the huge number of sequenced genomes now available.
We hope the CNV data we released we will be useful to others, and look forward to applications that use the many other improved genome references now being constructed.
Besides the data, the establishment of methods and formats were huge, under appreciated advances.
Yes! I bore the students in our intro to computational genomics class with stories about the scary days of working with Solexa data prior to the SAM/BAM format. BAM, VCF--all standards that have enabled so much
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