Tag: RefSeq

Bioinformatics Analysis of Viral Metagenomic Sequencing

Viral metagenomics is the study of viruses in environmental and biological samples by utilizing next generation sequencing that generates very large data sets. Viral metagenomics analyzes viral sequences to deduce the impact of viruses on the environment of human health. Unlike amplicon sequencing, metagenomics obtains and investigates genetic material directly…

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gff file from NCBI RefSeq GCF dataset has an invalid format

Thank you for noticing this. It is indeed an issue in the GFF3 file. The root of the problem is it’s a gene that is impossible to correctly represent in GFF3 because it incorporates sequence from both strands via trans_splicing. The complexity of this gene can be seen on the…

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EMDB < EMD-28585

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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First detection of Ixodiphagus hookeri (Hymenoptera: Encyrtidae) in Ixodes ricinus ticks (Acari: Ixodidae) from multiple locations in Hungary

Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: A review. Front. Public Health doi.org/10.3389/fpubh.2021.715759 (2021). Article  Google Scholar  Jongejan, F. & Uilenberg, G. The global importance of ticks. Parasitology 129, S3–S14 (2004). Google Scholar  Hornok, S., Kováts, D., Horváth, G., Kontschán, J….

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EMDB < EMD-13594

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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EMBOSS: dbxflat

EMBOSS: dbxflat dbxflat   Function Index a flat file database using b+tree indices Description dbxflat indexes a flat file database of one or more files, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb. Usage Here is a sample session with dbxflat…

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“Error parsing strand (?) from GFF line” happenning in gffread, stringtie and cufflinks

“Error parsing strand (?) from GFF line” happenning in gffread, stringtie and cufflinks 0 Hi! I’m working with various genomic data and while trying to use gffread, stringtie and cufflinks I went through the same error: Error parsing strand (?) from GFF line: NC_037304.1 RefSeq gene 58315 59481 . ?…

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Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Pfeffer C, Larsen S, Song J, Dong M, Besenbacher F, Meyer RL, et al. Filamentous bacteria transport electrons over centimetre distances. Nature. 2012;491:218–21. Article  CAS  Google Scholar  Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol. 2022;20:5–19. Article  CAS  Google Scholar  Bjerg JT, Boschker…

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KEGG T01001: 5742

Entry 5743              CDS       T01001                                  Symbol PTGS2, COX-2, COX2, GRIPGHS, PGG/HS, PGHS-2, PHS-2, hCox-2 Name (RefSeq) prostaglandin-endoperoxide synthase 2   KO K11987   prostaglandin-endoperoxide synthase 2 [EC:1.14.99.1] Organism hsa  Homo sapiens (human) Pathway hsa00590   Arachidonic acid metabolism hsa01100   Metabolic pathways hsa04064   NF-kappa B signaling pathway hsa04370   VEGF signaling pathway hsa04625   C-type lectin receptor signaling pathway hsa04657  …

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Human hg38 chr19:11,216,461-11,670,150 UCSC Genome Browser v442

     Custom Tracks 1806hidedensefull 468hidedensefull BT20hidedensefull BT474hidedensefull MCF7hidedensefull T47Dhidedensefull    Mapping and Sequencing Base Positionhidedensefull p13 Fix Patcheshidedensesquishpackfull p13 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow RefSeq Acchidedensesquishpackfull…

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RefSeq predicted transcripts/proteins alterations compared to genomic sequence

Hey! I’m trying to do some comparative genomics on different vertebrate proteins (cetaceaens whales more specifically). So I downloaded several RefSeq protein fasta’s for the proteins of interest in different cetacea species from NCBI. To check if there are any “weird” proteins (e.p. truncated or premature stopped proteins), I aligned…

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Classifying shotgun metagenomes with 16S rRNA database.

Hello dear all. My question is for people experienced in metagenomic analysis of complex microbial communities such as in soil. Suppose I have several soil shotgun metagenomes and I need to classify all of it reaching maximum possible diversity stored in my data. As far as I know, current full-genome…

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Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, Sun S, Xie X, Lai B, Su Y, Lu Y, Yang H, Huang T, Deng W, Nielsen R, Ren J,…

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Where did my .zip file get downloaded to?

Where did my .zip file get downloaded to? 0 (bio) nyck33@nyck33-IdeaPad-Gaming-3-15ACH6:~/Documents/Bioinformatics/ncbi$ datasets download virus protein S –filename spike-protein.zip Downloading: spike-protein.zip 13.6MB 105kB/s Downloading: spike-protein.zip 13.6MB done Use datasets download virus protein <command> –help for detailed help about a command. (bio) nyck33@nyck33-IdeaPad-Gaming-3-15ACH6:~/Documents/Bioinformatics/ncbi$ unzip spike-protein.zip -d spike-protein unzip: cannot find or open…

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EMDB < EMD-20433

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Unexpected absence of ribosomal protein genes from metagenome-assembled genomes

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article  PubMed  Google Scholar  Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…

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How to retrieve all genes of interest from GenBank?

How to retrieve all genes of interest from GenBank? 1 Hello Bioinformagicians! My goal is to create a phylogenetic tree using mitochondria genes of ticks. I’ve recently use genes taken from Refseq complete genomes. However, I want to include gene sequences that may not be part of complete genomes. How…

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KEGG T00005: YNL036W

Entry YNL036W           CDS       T00005                                  Symbol NCE103, NCE3 Name (RefSeq) carbonate dehydratase NCE103   KO K01673   carbonic anhydrase [EC:4.2.1.1] Organism sce  Saccharomyces cerevisiae (budding yeast) Pathway sce00910   Nitrogen metabolism sce01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:sce00001] 09100 Metabolism  09102 Energy metabolism   00910 Nitrogen metabolism    YNL036W (NCE103)Enzymes [BR:sce01000] 4. Lyases  4.2  Carbon-oxygen lyases   4.2.1  Hydro-lyases    4.2.1.1  carbonic anhydrase     YNL036W (NCE103) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: …

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Question 1.docx – Question 1 a) What is the first listed RefSeq mRNA sequence for human CRX? Provide your answer in “FASTA” format. Answer: Homo sapiens

Question 1a) What is the first listed RefSeq mRNA sequence for human CRX?Provide your answer in “FASTA”format.Answer:Homo sapiens cone-rod homeobox (CRX), mRNANCBI Reference Sequence: NM_000554.6GenBankGraphics>NM_000554.6 Homo sapiens cone-rod homeobox (CRX), mRNACCTTCAGCCTCTGCTGTCTGGCCGCTCTGTCTAGGTCCTGGGCCACGGGAGAGCCCCGTCCCTCCTTTCTGAAGGCCCCCTGACTTGGGCCTCAGTGTCCCCGAAGATCATGATGGCGTATATGAACCCGGGGCCCCACTATTCTGTCAACGCCTTGGCCCTAAGTGGCCCCAGTGTGGATCTGATGCACCAGGCTGTGCCCTACCCAAGCGCCCCCAGGAAGCAGCGGCGGGAGCGCACCACCTTCACCCGGAGCCAACTGGAGGAGCTGGAGGCACTGTTTGCCAAGACCCAGTACCCAGACGTCTATGCCCGTGAGGAGGTGGCTCTGAAGATCAATCTGCCTGAGTCCAGGGTTCAGGTTTGGTTCAAGAACCGGAGGGCTAAATGCAGGCAGCAGCGACAGCAGCAGAAACAGCAGCAGCAGCCCCCAGGGGGCCAGGCCAAGGCCCGGCCTGCCAAGAGGAAGGCGGGCACGTCCCCAAGACCCTCCACAGATGTGTGTCCAGACCCTCTGGGCATCTCAGATTCCTACAGTCCCCCTCTGCCCGGCCCCTCAGGCTCCCCAACCACGGCAGTGGCCACTGTGTCCATCTGGAGCCCAGCCTCAGAGTCCCCTTTGCCTGAGGCGCAGCGGGCTGGGCTGGTGGCCTCAGGGCCGTCTCTGACCTCCGCCCCCTATGCCATGACCTACGCCCCGGCCTCCGCTTTCTGCTCTTCCCCCTCCGCCTATGGGTCTCCGAGCTCCTATTTCAGCGGCCTAGACCCCTACCTTTCTCCCATGGTGCCCCAGCTAGGGGGCCCGGCTCTTAGCCCCCTCTCTGGCCCCTCCGTGGGACCTTCCCTGGCCCAGTCCCCCACCTCCCTATCAGGCCAGAGCTATGGCGCCTACAGCCCCGTGGATAGCTTGGAATTCAAGGACCCCACGGGCACCTGGAAATTCACCTACAATCCCATGGACCCTCTGGACTACAAGGATCAGAGTGCCTGGAAGTTTCAGATCTTGTAGAGGACGCAGTCTCCATCTCTCTCCATCGGGCCTCGGGACCC Read more here: Source link

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Number of sequences in RefSeq.

Number of sequences in RefSeq. 2 Dear colleagues I can not understand. When I download all the genomic sequences from the refseq database, after counting, I see that there are much fewer records than presented in the release (123394 organisms ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release214.txt). What am I doing wrong? 1. wget ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt 2….

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Building a Simulated Metagenomic Dataset

Building a Simulated Metagenomic Dataset – HackMD       Published Linked with GitHub — tags: ‘JPL: Genetic Inventory Project’ — # Building a Simulated Metagenomic Dataset Here we’ll create a simulated metagenomic datasets for controlled testing. This dataset was used to determine the Kraken 2 confidence score that best…

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RefSeq release 214 is available! – NCBI Insights

RefSeq release 214 is now available online, from the FTP site, and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of September 12, 2022, and contains 328,588,569 records, including 239,609,016 proteins, 47,387,931 RNAs, and sequences from 123,394 organisms. The release is provided in…

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KEGG T01001: 4171

Entry 4171              CDS       T01001                                  Symbol MCM2, BM28, CCNL1, CDCL1, D3S3194, DFNA70, MITOTIN, cdc19 Name (RefSeq) minichromosome maintenance complex component 2   KO K02540   DNA replication licensing factor MCM2 [EC:5.6.2.3] Organism hsa  Homo sapiens (human) Pathway hsa03030   DNA replication hsa04110   Cell cycle Disease H00604   Deafness, autosomal dominant Brite KEGG Orthology (KO) [BR:hsa00001] 09120 Genetic Information Processing  09124…

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KEGG T02666: 101290786

Entry 101298727         CDS       T02666                                  Name (RefSeq) triacylglycerol lipase SDP1   KO K14674   TAG lipase / steryl ester hydrolase / phospholipase A2 / LPA acyltransferase [EC:3.1.1.3 3.1.1.13 3.1.1.4 2.3.1.51] Organism fve  Fragaria vesca (woodland strawberry) Pathway fve00100   Steroid biosynthesis fve00561   Glycerolipid metabolism fve00564   Glycerophospholipid metabolism fve00565   Ether lipid metabolism fve00590   Arachidonic acid metabolism fve00591   Linoleic…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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Index of /Rsubread/annot

Name Last modified Size Description Parent Directory   –   chm13v2.0_RefSeqStri..> 2022-08-22 01:51 2.0M   chm13v2.0_RefSeq_12A..> 2022-08-22 01:51 2.5M   code/ 2022-08-22 01:53 –   hg38_RefSeqStrict_22..> 2022-08-22 01:51 2.3M   hg38_RefSeq_22Apr202..> 2022-08-22 01:51 3.0M   mm10_RefSeqStrict_22..> 2022-08-22 01:51 2.0M   mm10_RefSeq_22Jun202..> 2022-08-22 01:51 2.5M   mm39_RefSeqStrict_23..> 2022-08-22 01:51 1.9M  …

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New annotations in RefSeq – NCBI Insights

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-six new annotations in RefSeq for the following organisms: Anopheles coluzzii (mosquito) Anopheles funestus (African malaria mosquito) Astyanax mexicanus (Mexican tetra) Athalia rosae (coleseed sawfly) Bactrocera dorsalis (oriental fruit fly) Brassica napus (rape) Brienomyrus brachyistius (bony fish) Canis lupus dingo (dingo) (pictured) Caretta…

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KEGG T01015: 107278078

Entry 4330855           CDS       T01015                                  Name (RefSeq) auxin-responsive protein SAUR32   KO K14488   SAUR family protein Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa04075   Plant hormone signal transduction Brite KEGG Orthology (KO) [BR:osa00001] 09130 Environmental Information Processing  09132 Signal transduction   04075 Plant hormone signal transduction    4330855 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Auxin_inducible Motif Other DBs…

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UniProt: A0A6I9ZUN5_ACIJB

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

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Gene Set – TNFSF10

Dataset MSigDB Cancer Gene Co-expression Modules Category transcriptomics Type co-expressed gene Description tumor necrosis factor (ligand) superfamily, member 10|The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein preferentially induces apoptosis in transformed and tumor cells, but does not…

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How to identify locus_tag by using RefSeq protein info (WP_*)

How to identify locus_tag by using RefSeq protein info (WP_*) 0 Hi, I would like to know the locus tag of a protein annotated with RefSeq (WP_*). For example, I would like to identify the genomic location of a protein (WP_073031595.1) and also know its adjacent proteins. The GenBank file…

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can gff2 reference used in htseq-count?

Dear all We are recently working with E.coli plasmid and tried to summarize the gene counts from our RNA-Seq samples. The short reads were mapped to E.coli plasmid using tophat which generated bam files accordingly. However, we were unable to obtain a gff3 version of our target plasmid genome, the…

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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RefSeq Release 212 is available!

RefSeq Release 212 is now available online, from the FTP site and through NCBI’s Entrezprogramming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of May 2, 2022, and contains 314,915,153 records, including 229,417,182 proteins, 44,805,833 RNAs, and sequences from 119,373 organisms. The release is provided in several directories…

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Transcription Start Site

Transcription Start Site 2 What are the best databases to check out the transcription start sites of specific genes in human genome? TSS • 130 views wget -q -O – “http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz” | gunzip -c | awk ‘(int($7)< int($8)) {if($4==”+”) {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,$7,int($7)+1,$2,$4);}else {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,int($8)-3,$8,$2,$4);}}’ chr1 69090 69091 ENST00000335137.3 + chr1 139306 139309 ENST00000423372.3…

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Summary of Fusobacterium nucleatum MJR7757B, version 26.0

Summary of Fusobacterium nucleatum, Strain MJR7757B, version 26.0 Tier 3 Uncurated Database Summary: This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Fusobacterium nucleatum MJR7757B, as obtained from RefSeq (annotation date: 04-APR-2017). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software…

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C1qBP antibody [GT1250] | Axil Scientific

This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX02847 Brand GeneTex Application IHC-PWB Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. For…

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EpCAM antibody [G8.8] | Axil Scientific

This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX80323 Brand GeneTex Application FACSICC/IFIHC-FrIPWB Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. For…

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SMAD4 antibody | Axil Scientific

This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX03325 Brand GeneTex Application IHC-P Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. Store…

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NCBI RefSeq representative and reference genomes precalculated in PhenDB

News PhenDB now contains in the “Browse” section the trait precalculations for the reference genomes and representative genomes in NCBI RefSeq. The trait prediction results can be filtered by user-specific criteria for minimal prediction confidence and minimal balanced accuracy. Three figures demonstrate the number of positive and negative predictions for…

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Easy Way To Get 3′ Utr Lengths Of A List Of Genes

Easy Way To Get 3′ Utr Lengths Of A List Of Genes 4 Hi, as the title says really, I’m wondering if there is any tool available that would allow me to drop in a list of say entrez gene ids and get their corresponding 3′ UTR lenghts? Thanks for…

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List of human protein coding genes with given name (known function?)

List of human protein coding genes with given name (known function?) 2 Hello, To put it simply, I am doing differential expression analysis on human RNA-seq data and I want to focus my analysis of genes that are: 1) Protein coding, so no SNOR or MIR 2) Genes with a…

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Having issue running TransposonPSI

Having issue running TransposonPSI 0 Hi, I have tried running the transposonPSI on our sever several times and always come back with an error message below. Is there anyone that knows how this can be resolved. Your help and contribution would be much appreciated. (base) taiwo@zetaadmin:/home/programs/repeatmasker/TransposonPSI_08222010$ sudo ./transposonPSI.pl /home/taiwo/Genome_Annotations/funannotate_E34/genome.proteins.fasta prot…

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Ribon Therapeutics hiring Principal Scientist Bioinformatics in Cambridge, MA, US

About Ribon Therapeutics Ribon is a clinical-stage biotechnology company dedicated to the discovery and development of first-in-class small molecule inhibitors to block the fundamental ability of cancer cells to survive under stress. Job Description Ribon Therapeutics, a clinical biopharmaceutical company focused on targeting stress pathways to develop novel cancer therapeutics,…

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does not contain a ‘gene’ attribute

htseq-count returns : does not contain a ‘gene’ attribute 1 Dear BIOSTAR community, I’m trying to make count matrix with htseq-count, htseq-count -s yes -t gene -i gene 01.sorted.sam annotation_cattle.gff > 01.txt even with –idattr=gene , it returns error: Error processing GFF file (line 1864255 of file annotation_cattle.gff): Feature gene-D1Y31_gp1…

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Annotation Forge Error: makeOrgPackageFromNCBI

Annotation Forge Error: makeOrgPackageFromNCBI 0 Hi, I just run a code inherited from a recent nature paper: github.com/RoundLab/Ost_CandidaRNASeq However, I got a lot of errors with annotation forge. Would you please help me? Yesterday, I had another error. Today I have rerun it, and I got another error. 🙁 library(“biomaRt”)…

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Download Assembled Genomes NOT in RefSeq

Download Assembled Genomes NOT in RefSeq 0 I have a list of NCBI accession numbers and I need to download the genome sequence (or assemblies) in FASTA format. I can accomplish this for genomes that are present in RefSeq using the following command: esearch -db nuccore -query GCF_900343155.1 | efetch…

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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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Sequence (annotation) databases in 2021

Forum:Sequence (annotation) databases in 2021 1 Hi everyone, So I know there are several threads on this topic already (or tangentially related to it). For example: But these threads are really old now. Things have probably changed quite significantly in the mean time. So I would like to start a…

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How to fix GTF files by adding specific strings into empty gene_id “”

How to fix GTF files by adding specific strings into empty gene_id “” 1 Hi, I want to repair GTF file by adding a unique string (such as Product name) to empty gene_id “”. I would really appreciate it if anyone could provide any solution. For example: grep -m1 ‘gene_id…

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