Tag: Liftoff

A live colony of human induced pluripotent stem cells fills the screen of a microscope. (Allen Institute Photo) Space: The final frontier … for stem cells? Seattle’s Allen Institute for Cell Science says cells from its collection are going into space for the first time on a private mission to…

Repeat masking for genome annotation 0 I am working on a (plant) genome annotation pipeline and would like some advice regarding repeat masking. My pipeline consists of running several ab-initio gene prediction tools (Augustus, GlimmerHMM and SNAP) + transcript alignment (PASA) + protein alignment (genomeThreader) evidence + gene liftover (liftoff),…

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

Scientists are growing stem cells in space in an effort to discover new ways to produce large batches of certain stem cells to treat a variety of diseases. Researchers from Cedars-Sinai Medical Center in Los Angeles are behind the program that delivered stem cells to the International Space Station (ISS)…

snpeff : wont recognize the gtf or gff3 files (runtime exception) 1 Hi, I am trying to build a custom databasee for snpeff. As instructed both in the forum and snpeff instructions, I did the following; Then I added the following into snpEff.config file # BG94_1 BG94_1.genome : BG94_1 Then…

Are there any alternatives to Liftoff – Mapping annotations (GFF/GTF) between assemblies 2 Hi, I am annotating closely related accession (varieties) using reference assembly (please note that I am using only a region, so that is the reason why you don’t see chromosome info). I really liked liftoff (ver 1.6.1:…

Blank output When converting GFF3 file to GTF using either gffread or AGAT 1 Hi, I am trying to convert gff3 file (please see below) to GTF. I used two tools suggested here gffread and agat here. #gff-version 3 Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 1 1345 . + . ID=gene_1;Name=Os01g0293800 gene;coverage=0.997;sequence_ID=0.982;extra_copy_number=0;copy_num_ID=gene_1_0 Bg_94-1_CX35|chr01_10700000_16500000…

Hi, I want to map annotations from rich gencode human gtf or gff3 to great apes’ genome. I tried to run liftoff (github.com/agshumate/Liftoff) but it returns error the below. Following the github issue’s post, I confirmed there’s no _db file before running, the annotation file is .gff3, the permission of…