Evolutionary Genomics | Akbarjon Rozimov

Top AI medical scientists Roland Eils and Irina Lehmann leave Germany for China Married researchers have published more than 1,000 peer-reviewed papers and are pioneers of artificial intelligence in medicine. Many are leaving, and nesting in China. I can’t imagine how China will become superpower in science. https://t.me/EvolutionaryGenomics

Yuqorida qanday qilib sekvens kompaniyadan ma'lumotni yuklab olishni aytgandim. Undan keyingi bosqich, sekvensni filtrlash, nima uchun filtrlash kerak? 1. Past sifatli sekvens; 2. Adapter kontaminatsiyasi. Odatda, Illumina short read sekvens assembly qilishdan oldin filtrlanadi, va bunda biz fastp dasturidan foydalanishimiz mumkin. Yuqorida filtrlash uchun human readable sodda *.pbs kodni yozdim. Fastp dasturining -i and -I funktsiyasi input ma'lumot uchun XX-1_1.fq.gz va XX-1_2.fq.gz uchun mos ravishda. Filterlangan sekvens -o va -O funtksiyalari kiritilgan holda yaratiladi. Bunda filterlangan sekvens original sekvens nomidan farq qilishi uchun odatda XX-1_1-clean.fq.gz, XX-1_2-clean.fq.gz deb yozishimiz mumkin, albatta bu sizni xohishingizga bog'liq. -w funktsiyasi esa bizni Linux serverimizda mavjud bo'sh CPU uchun. Fastp dasturi boshqa dasturlarga qaranganda ancha user-friendly. Filterdan oldingi va keyingi farqni .html va .json link orqali google tog'oda ko'rish mumkin. https://t.me/EvolutionaryGenomics

Can we bring back extinct animals? Several moths ago, an American company named the Colossal Biotechnology announced the resurrection of the Dire wolf. Interestingly, this company has been continuing its surprising news that they aimed to bring back extinct South Island giant moa (Dinornis robustus) through genetic engineering. To date, giant moa is a flightless bird roamed New Zealand before going extinct around 600 years ago. This highlights the shrinking prices in genome sequencing, editing and engineering, meanwhile the new era for resurrection technologies. However, the resurrected animal would not be like its own ancestral species. https://t.me/EvolutionaryGenomics

Genomik tadqiqotlarda ish yuqori hajmdagi sekvens ma’lumotlarni yuklab olishdan boshlanadi, bir necha Gb dan o’nlab Tb ma’lumotgacha. Bu holatda sekvens kompaniya sizga USB fleshkada yoki external terabaytda emas, aksincha kompaniyaning Onlayn kloudi orqali yuklab olishni so’raydi. Bunda sizning sekvens ma’lumotlaringiz kompaniyaning onlayn kloudiya joylanadi. Va sizga login parol beriladi. Bir necha software orqali yuklab olish mumkin. Yuqorida Ossutil dasturi orqali Linux tizimida qanday yuklab olishga misol keltirdim. #SequenceDownload https://t.me/EvolutionaryGenomics

Professional figuralar yaratishda Rstudio ga teng keladigani bo’lmasa kerak? Python ham qolishmaydi, ammo Rstudio aynan statistik figuralar yaratish uchun eng to’g’ri tanlov. https://t.me/EvolutionaryGenomics

Nice email at the end of day! Peer-review No. 3 Bir vaqtlari ayrim rus olimlari biz o’zbek olimlarini olim sifatida tan olishmas edi. Ushbu maqolada aynan rus olimlari tomonidan Kavkaz hududidan yangi baliq turi tasvirlandi, va maqola revyuverlari orasida men ham o’rin olgan edim. Bu shuni anglatadiki, o’zbeklardan ham dunyo tan oladigan yosh olimlar yetishib chiqyabdi. https://t.me/EvolutionaryGenomics

Jobni submit qildingiz, ammo yetarlicha CPU mavjud emas, va navbatda kutishingiz kerak. Bu payti ortiqcha ishlatilmayotgan CPU ni tekshirish uchun "pnodes" ishga keladi. Yuqorida pnodes ni yuritganimizda "node01" 4 CPU ishlatilmayotganini ko'rdik. Bunday vaqtda siz ishlayotgan skript 4 CPU dan yuqori bo'lsa "qdel" orqali kill qilib, 4 CPU ga to'g'rilab olsangiz bo'ladi. Kill qilish "qdel.XXX" orqali amalga oshiriladi. Va ishni qaytadan edit qilgandan so'nag "qsub" orqali qayta topshiriladi. #BashLinux https://t.me/EvolutionaryGenomics

Linux fayl sistemasi: umumiy ko'rinishda: asosiy ish boriladigan joy /home u yerda xohlagancha folder yaratib vazifalar bajariladi. #BashLinux

2. Faqat o'zingiz ishlayotgan joblarni tekshirmoqchi bo'lsangiz "qstat -u username" #BashLinux

1. Skriptingiz yurayotgani yoki navbatda turayotganini tekshirmoqchimisiz? "qstat -a" #BashLinux

https://t.me/EvolutionaryGenomics

Snow leopard - Panthera uncia is a big cat, distributed from western Tian Shan and Pamir mountains to eastern Xinjiang, and northern Altai (Russia, Mongolia) mountains; in southern Qinghai-Tibetan mountains to Himalaya. Snow leopard taxonomy is still controversial. The northern (Altai), western (Tian Shan, trans-Himalaya) and central subspecies (core Himalaya) was globally accepted. However, in this study, Chinese scientists assembled de novo chromosome-level genome and mapped 53 individuals’ whole-genome resequencing data, and filtered high-quality ~ 1.48 mln SNPs, average genome coverage 21.9-fold. The results of SNPs based phylogenetic tree, PCA and ADMIXTURE revealed two major lineages: northern and southern (Fig 1B). Northern lineage included Altai, Tian Shan (west and east) and Pamir populations, whereas southern lineage included Qinghai-Tibetan and core Himalaya populations. Previously accepted two northern and western subspecies nested in northern lineage, and central subspecies nested in southern lineage. The Fst value between northern and western lineage was 0.126, a bit lower than most of other studies to distinguish two subspecies thresholds. Admixture analysis also supported two lineages, cv error was appointed to be lowest in K=2, interestingly authors re-confirmed recent admixture of snow leopards between Xinjiang and Tajikistan, which was observed in previous studies too. Two lineages of snow leopards can be also seen in their distribution, the Gobi desert between Mongolia and China, the Taklamakan desert between western and central Himalay play as a geographical barriers. This boundary is an important geographical barrier for food competition and survival of animals. In conclusion, this part of study indicated that snow leopards shall be considered as two subspecies, rather than three subspecies. https://t.me/EvolutionaryGenomics