Tag: AGAT

Evidence of an intracellular creatine-sensing mechanism that modulates creatine biosynthesis via AGAT expression in human HAP1 cells

Cell lines and reagents HAP1 cells used to generate the reporter cells were grown from a frozen stock of HAP1 (C859) passage 6 purchased from Horizon Discovery LTD (Cambridge, UK). Iscove’s media (Ref: 098–150, Wisent) supplemented with 10% Fetal Bovine serum (Multicell) was used to grow HAP1 cells. All cells…

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Fastest way to convert BED to GTF/GFF with gene_ids?

This is probably a duplicated question from: How To Convert Bed Format To Gtf? How to convert original BED file to a GTF ? Converting different annotation file formats (GTF/GFF/BED) to each other How to change scaffold.fasta file or scaffold.bed file to GTF file? Convert bed12 to GFF convert bed12…

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Yes .. BBMap can do that!

NOTE: This collection was originally posted at SeqAnswers.com. Creating a copy here to preserve the information.Part I is available here: Yes .. BBMap can do that! – Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)Part II is available here: Yes .. BBMap can…

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Adding functional annotation and meta-data of MAKER/BRAKER GFF

Adding functional annotation and meta-data of MAKER/BRAKER GFF 0 Happy new year, 2023. I am doing genome assembly and annotation. I have a problem doing the functional annotation part of it since I am new and still learning this. I have done the following: Assembled the genome (using Verkko and…

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

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GTF files from Ensembl Releases 105 and 106 unsorted

There is nothing wrong with these files. Sort (as any GTF): zcat Homo_sapiens.GRCh38.105.gtf.gz \ | awk ‘$1 ~ /^#/ {print $0;next} {print $0 | “sort -k1,1 -k4,4n -k5,5n”}’ \ | bgzip > Homo_sapiens.GRCh38.105_sorted.gtf.gz That having said, if you need the file being strictly coordinate-sorted then you always have to do…

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Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Orr, H. A. The genetic theory of adaptation: A brief history. Nat. Rev. Genet. 6, 119–127 (2005). Article  CAS  PubMed  Google Scholar  Dillon, M. E. & Lozier, J. D. Adaptation to the abiotic environment in insects: the influence of variability on ecophysiology and evolutionary genomics. Curr. Opin. Insect Sci. 36,…

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Contig order rearranged agat

Contig order rearranged agat 0 Hi, I annotated a genome with prokka and while converting to GTF with agat, I get the following error: => Version of the Bioperl GFF parser selected by AGAT: 3 gff3 reader error level1: No ID attribute found @ for the feature: … 1 warning…

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adding features to gtf file using agat tool function

I m trying to use this agat which adds new attributes from tsv to gtf file. My file formats are as such input tsv which is my reference file gene_id Entrez_ID ENSCAFG00845006432 399518 ENSCAFG00845002136 399530 ENSCAFG00845029798 399544 ENSCAFG00845011460 399545 ENSCAFG00845001610 399653 ENSCAFG00845013158 403157 ENSCAFG00845014982 403168 ENSCAFG00845021967 403170 ENSCAFG00845019241 40340 Next…

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gff3 to gtf

gff3 to gtf 1 Hello everyone, I am trying to convert gff3 file to gtf file for that I used the command below:agat_convert_sp_gff2gtf.pl -i input.gff3 -o genes.gtf But it did not work. Can anyone help me with this issue? gtf gff3 • 28 views • link updated 1 hour ago…

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Gene prediction in the era of long read sequencing data and many reference genomes

With the availability and affordability of long read sequencing it has become possible to create many reference genomes. For individuals of the same species, or for many species. See e.g. how Hifiasm can be used with a single command to create a reference genome in a few hours or days…

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How to extract summary statistics from GFF3 /GTF file?

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…

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Adding ‘gene_name’ attribute to each row of GTF/GFF file (missing for CDS, transcript, and exon rows)

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…

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gff to gtf missing gene id

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 . + ….

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Maker Gff3 file issues

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…

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Error while converting GFF file to GTF using AGAT

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…

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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

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,…

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Bioinformatics Answers

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…

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Package conflicts installing AGAT

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…

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Line length limit on input FASTA file: 65,536 characters (limit imposed by bioperl)

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:…

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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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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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GRCh37 GFF filter transcript isoforms by RefSeq Select tag or longest

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,…

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