Tag: AGAT

Hi! You could try using the gffutils Python library as an alternative to the AGAT toolkit for extracting summary statistics from GFF3/GTF files. gffutils is a flexible and efficient library for working with GFF and GTF files in a variety of formats. Here’s an example of how to use gffutils…

Hello, Can someone please help me with this issue I’m having? Thank you in advance! I have a GFF file, and I have the gene_name attribute in my GFF file, but it’s only present for each gene entry (i.e., it’s absent from the transcript, cds, and exon rows). I want…

gff to gtf missing gene id 1 Hi, I was trying my hand at annotating a genome using prokka, and I’ve converted the output gff file to gtf (gffread file.gff -T -o file.gtf) and this is what my gtf file looks like: CP001095.1 prokka transcript 210 1712 . + ….

Maker Gff3 file issues 1 Hi community, This is really a technical question, I hope it is OK to post it here… I am trying to import the gff3 file from Maker to my Jbrowse to view the annotations. I am using the maker2jbrowse script and getting constant errors. There…

Error while converting GFF file to GTF using AGAT 0 Hi I am trying to convert a gff file to gtf file which I want to use for STAR. I tried AGAT(latest version) to convet but it gives me a series of error(mailny tow types) .I have attached the error…

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

Comment: why I download .sra file throught the SraRunInfo.csv but got files with extensi by GenoMax 109k SRA data has since moved to cloud so the links above are likely referring to the cloud data location. Those appear to be `.sra` format file… Comment: why I download .sra file throught…

Hi, I am not an expert in Windows and Linux OS. I would like to try to install AGAT on my computer. The OS is a Windows7 (64 bit installation) and I have ANACONDA Navigator 1.10.0 To install the software I have opened the ANACONDA Navigator dashboard and I have…

Hello, I’m trying to run the following command: agat_sp_extract_sequences.pl -g JU2526_Y39G10AR.22.gff -f JU2526*_region.fa -p And it throws the following error: ————- EXCEPTION: Bio::Root::Exception ————- MSG: Each line of the file must be less than 65,536 characters. Line 2 is 67824 chars. STACK: Error::throw STACK: Bio::Root::Root::throw /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::DB::IndexedBase::_check_linelength /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757 STACK:…

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…

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…

GRCh37 GFF filter transcript isoforms by RefSeq Select tag or longest 0 Dear all, I tried to filter the “RefSeq Select” transcript isoforms in the GRCh37.p13 human genome annotation gff (GCF_000001405.25_GRCh37.p13_genomic.gff.gz). Specifically my goal is to retain for each gene a transcript isoform with a tag=RefSeq Select attribute if exists,…