Tag: Liftoff

Researchers Grow Stem Cells Aboard International Space Station In New Study

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)…

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wont recognize the gtf or gff3 files (runtime exception)

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…

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Are there any alternatives to Liftoff

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:…

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Blank output When converting GFF3 file to GTF using either gffread or AGAT

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…

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local variable ‘feature_db’ referenced before assignment

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…

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