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brent pedersen proslijedio/la je Tweet
Introducing "Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED" with
@samkovaka@timp0 et al. Does selective enrichment and depletion of any targeted genomic region purely in software for@nanopore sequencing.https://www.biorxiv.org/content/10.1101/2020.02.03.931923v1 …Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
brent pedersen proslijedio/la je Tweet
MMRF CoMMpass has ~1000 shallow genomes, exomes and RNA-Seq. The cells are sorted and hence are high purity.
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brent pedersen proslijedio/la je Tweet
Geuvadis is basically rna-seq from 465 1kg samples
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what is the largest set of broadly usable (including dbgap, ICGC) human samples for which there is both WGS and RNA-Seq?
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brent pedersen proslijedio/la je Tweet
I like Cranefoot for drawing pedigrees. http://www.finndiane.fi/software/cranefoot/ …
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here are the rules for inference:https://github.com/brentp/somalier/wiki/pedigree-inference …
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somalier helps to find sample swaps. it was still difficult to rectify bad information. as of pending release, it will infer pedigree structure for first-degree relatives (which can extend to large pedigrees) can infer sibs without parents present and can join families.
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super-pedigree. drawn with
@Yutaka__Masuda 's awk -> dot 1-linerpic.twitter.com/395oogQ1jB
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tracking solutions here:https://gist.github.com/brentp/b6b437caedff22c3c4038cf9bebec03d …
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brent pedersen proslijedio/la je Tweet
Just for your information: one-linear using Graphviz (no web interface) for pedigree drawing: awk -v family=1 'BEGIN{print "digraph fam{"} family==1{if($3!="0"){printf("%s -> %s;\n",$3,$2)}if($4!="0"){printf("%s -> %s;\n",$4,$2)}} END{print "}"}' test.ped | dot -Tpng -o fam.png
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wanted: an online tool where one can paste a pedigree/fam file and get a pedigree drawing.
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brent pedersen proslijedio/la je Tweet
HG002 data release from
@HumanPangenome.@PacBio HiFi, CLR,@nanopore PromethION, GridION,@illumina Hi-C, Strand-seq,@bionanogenomics opmaps... CC0-licensed. Benchmarking to inform production sequencing recipehttps://github.com/human-pangenomics/HG002_Data_Freeze_v1.0 …Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
brent pedersen proslijedio/la je Tweet
Asking 400 students to send me cell biology memes may be my best idea of 2020.
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percent of non-PASS variants from GATK is much higher on chrX . is this widely known?
@sexchrlab@TimWebster17 ?pic.twitter.com/Mw9i9V80IT
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brent pedersen proslijedio/la je TweetHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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brent pedersen proslijedio/la je Tweet
currently testing a new nextflow script https://gist.github.com/lindenb/6f6513a69d508252b899cf43f119f743 … for a few bams using
@brent_p 's somalier . "fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs"Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
brent pedersen proslijedio/la je Tweet
Finally managed to get URMAP running from start to finish. The good news: it does align reads fast. The bad news: it appears to be in an alpha state lacking core features necessary to really evaluate its impact on downstream analyses. (1/n)https://twitter.com/biorxivpreprint/status/1217091899900731392 …
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I am sympathetic to those trying to make non-commercial software licenses work, but am seeing this. Does this seem unusable to anyone else?pic.twitter.com/HdxZrq015Y
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d-PBWT: dynamic positional Burrows-Wheeler transformhttp://disq.us/t/3lbrv9w
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