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#genomics

1 post1 participant0 posts today
flypapers

📰 "A genome-wide MAGIC kit for recombinase-independent mosaic analysis in Drosophila"
biorxiv.org/content/10.1101/20
#Drosophila #Genomics

bioRxiv · A genome-wide MAGIC kit for recombinase-independent mosaic analysis in DrosophilaMosaic analysis has been instrumental in advancing developmental and cell biology. Most current mosaic techniques rely on exogenous site-specific recombination sequences that need to be introduced into the genome, limiting their application. Mosaic analysis by gRNA-induced crossing-over (MAGIC) was recently developed in Drosophila to eliminate this requirement by inducing somatic recombination through CRISPR/Cas9-generated DNA double-strand breaks. However, MAGIC has not been widely adopted because gRNA-markers, a required component for this technique, are not yet available for most chromosomes. Here, we present a complete, genome-wide gRNA-marker kit that incorporates optimized designs for enhanced clone induction and more effective clone labeling in both positive MAGIC (pMAGIC) and negative MAGIC (nMAGIC). With this kit, we demonstrate clonal analysis in a broad range of Drosophila tissues, including cell types that have been difficult to analyze using recombinase-based systems. Notably, MAGIC enables clonal analysis of pericentromeric genes and deficiency chromosomes and in interspecific hybrid animals, opening new avenues for gene function study, rapid gene discovery, and understanding cellular basis of speciation. This MAGIC kit complements existing systems and makes mosaic analysis accessible to address a wider range of biological questions. ### Competing Interest Statement The authors have declared no competing interest. Office of the Director, https://ror.org/00fj8a872, R24OD031953
Luke Pembleton

1/🧵 Ok, so I finally figured out the interesting (i.e. painful) error I’ve been chasing in my #Nextflow genomic mapping pipeline the past few days.
Basically, I’ve got hundreds of bwa mem mapping jobs running as separate processes in Docker containers, grouped on large AWS EC2 instances. Seemingly randomly some samples would fail during the subsequent mark duplicates process due to issues with the read group (@RG) headers.
#bioinformatics #genomics

Bibliolater 📚 📜 🖋

🧬 **Phoenician culture spread mainly through cultural exchange**

"_Individuals with North African ancestry lived next to and intermingled with a majority of people of mainly Sicilian-Aegean ancestry in all sampled Punic sites, including Carthage. Moreover, genetic networks across the Mediterranean suggest that shared demographic processes—such as trade, intermarriage, and population mixing—played a critical role in shaping these communities._"

🔗 mpg.de/24574685/0422-evan-phoe.

#Genetics #Ancient #DNA #Genomics #Science #Phoenicia #Culture @science

www.mpg.dePhoenician culture spread mainly through cultural exchangeStudy challenges long-held assumptions about the Mediterranean Phoenician-Punic civilization, one of the most influential maritime cultures in history
Luke Pembleton

Anyone else finding the sequencing costs appear to be getting more expensive rather then continuing to decline. I'm thinking its likely related to inflation, wages and current US uncertainty...? oh and Illumina and alike only delivering true reduced cost/GB on large scale flowcells, which aren't suitable for many small to medium size projects...
#genomics #bioinformatics

Eli Roberson (he/him)

#Genomics
#Bioinformatics
#Academia

Beware US academic coders. If you have collaborators contributing code from a sanctioned region, your repos may be locked.

See mastodon.social/@organicmaps/1

The kicker is that the US is leaning authoritarian and all in on censorship. If Canada or Mexico become sanction targets and you have code pushes from there, Microsoft will lock you out of your GitHub accounts.

MastodonOrganic Maps (@organicmaps@mastodon.social)Attached: 1 image We have a temporary glitch with GitHub—probably some contributor was geolocated in a sanctioned region (no details yet). All required documents to unlock the account have been uploaded. Don't blame Microsoft/GitHub - it is just U.S. law. Please be patient. It should be unblocked soon.
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