Tag: StringTie

Tool:ChatGPT optimized for bioinformatics questions 1 Hey everyone! I launched a new chatbot today that is bioinformatics focused! It’s trained on bioinformatics content and should help debug / ideate much faster for you than vanilla ChatGPT. Check it out here: ai.tinybio.cloud/chat Thanks! gpt • 165 views • link updated 1…

Docker Error while running nf-core/rnaseq pipeline 1 I have run a nf-core pipeline with the following parameters: nextflow run nf-core/rnaseq -r 3.10.1 –input samplesheet.csv –outdir outputlatest –fasta chr22_with_ERCC92.fa -profile docker –gtf chr22_with_ERCC92.gtf –skip_multiqc true –skip_dupradar true –skip_stringtie true –aligner star_salmon –pseudo_aligner salmon –max_memory 3.5GB –max_cpus 4 Receiving an error related…

Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article  ADS  CAS  PubMed  Google Scholar  Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article  Google Scholar  Darwin, C. The Descent of Man, and Selection…

I am analyzing PacBio IsoSeq data and I am using StringTie to assemble transcripts. I noticed the difference in the output files when I add a reference genome annotation (-G option in StringTie). In general I have less transcripts assembled when I give as imput reference genome annotation and I…

Name Last modified Size Description Parent Directory   –   e2t.ctab 2023-04-28 14:22 2.7M   e_data.ctab 2023-04-28 14:22 14M   heart-hisat2_stats.txt 2023-04-28 13:58 647   heart.cov_refs.gtf 2023-04-28 14:22 5.4M   heart.gtf 2023-04-28 14:22 38M   heart.sorted.bam 2023-04-28 14:07 12G   heart.sorted.bam.bai 2023-04-28 14:11 2.0M   heart_checksums.md5 2023-04-28 14:23 484  …

StringTie across datasets 0 Hello! I am working on assembling novel transcripts through StringTie for various human RNA-Seq datasets. But, I am not finding any common novel transcripts across the datasets. Am I missing something or is the possibility of finding any common transcripts really low? Any suggestion is welcome!…

Generate hashes for all sequences in a FASTA file 1 Hello! I am working on novel transcripts assembled from RNA-Seq data, using Stringtie. However, since stringtie “MSTRG” ids are poorly conserved across runs, I wanted to implement a strategy that converts all transcript sequences in a FASTA file to a…

Count Matrix normalisation for downstream analysis and for creating heatmap of targeted genes 0 Hello Everyone! I have a count matrix generated from stringtie (from FPKM to readcount using prepDE.py3 of stringtie). i would like to create heatmap of targeted genes across samples. My questions are : 1) Before creating…

Annotate CDS and UTR given transcript 1 I am annotating a new genome and I am combining several sources of information for the annotation. It combines a de novo annotation as well as lifting over annotations from closely related species. I have been using GFFCompare (ccb.jhu.edu/software/stringtie/gffcompare.shtml) to merge GFF files….

Error when running prepDE.py in Stringtie 0 Hi, I was trying to execute prepDE.py and Command: prepDE.py -i sample_gene.lst I get the following error: $ prepDE.py -i sample_gene.lst Error: could not locate transcript ENST00000618889 entry for sample CASE2 Traceback (most recent call last): File “/data/leehyobin/Step0_RawFile/stringtie/stringtie/prepDE.py”, line 284, in geneDict.setdefault(geneIDs[i],{}) #gene_id…

Hello, – I ran stringtie and obtained *merge.gtf* as a result. Now, I want to run *prepDE.py3* to obtain *gene.csv* and *transcript.csv*. I thought *prepDE.py3* was a function that was embedded together with *stringtie* when I installed it. – However, when I type “*./prepDE.py3*” or “*prepDE.py3*” in the Ubuntu terminal,…

Nextflow rnaseq finishing early 0 Hi I’m running the RNA-seq pipeline from nextflow and I have been running it without problems until this dataset it just stops prematurely saying it has finished when it doesn’t even aligns the reads with salmon. Any ideas what may be going on? I have…

Error parsing strand (?) from GFF line 0 I am trying to assemble RNA transcripts using stringtie and facing the following error. Error parsing strand (?) from GFF line: NC_037304.1 RefSeq gene 58315 59481 . ? . ID=gene-DA397_mgp34;Dbxref=GeneID:36335702;Name=nad1;exception=trans-splicing;gbkey=Gene;gene=nad1;gene_biotype=protein_coding;locus_tag=DA397_mgp34;part=2 my comand is : stringtie -p 8 -G Genome/arab_thaliana.gtf -o Assemble/NR1.gtf –l…

Stringtie does not work with NCBI GTF file? 1 Hi all, I wanted to rerun my DGE analysis to see if there were any differences between HTseq-count -> edgeR and StringTie-Ballgown. However, when I tried to run my stringtie command using the same BAM file, I got an error: “Error:…

Nextflow Stringtie: command not found Error 1 Im trying to use stringtie in my nextflow pipeline and I’ve tried to write the stringtie code and have gotten this error. Im not sure how to correct this. Any help would be greatly appreciated! nextflow rna-seq stringtie • 25 views That’s not…

Please give me a grep command to get Gene IDS and TPM values from a stringtie output gtf file 2 Hi, Could anyone please give me a grep command to get gene_id and respective TPM values from a string tie output file. My result output file looks like the following…

Grabowski P, Zaug A, Cech T. The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena. Cell. 1981;23(2):467–76. Article  CAS  PubMed  Google Scholar  Ye C, Chen L, Liu C, Zhu Q, Fan L. Widespread noncoding circular RNAs in plants. New Phytol….

I have a question for deg analysis tools 1 Hi. I’m going to do DEG analysis with tmp data that has already been normalized. I want to use a total of four tools; DESeq2, edgeR, Ballgown, Limma. But I already knew the raw count data can only be used in…

Ballgown Differential Transcript Expression Output Table 0 Hello everyone, I was wondering if anybody could help me understand the output I am getting using the StringTie –> Ballgown pipeline in order to measure differential transcript expression between two groups. My confusion some of the column name identifiers that the ballgown…

Bates, G. P. et al. Huntington disease. Nat. Rev. Dis. Primers 1, 15005 (2015). Article  Google Scholar  Shulman, J. M., De Jager, P. L. & Feany, M. B. Parkinson’s disease: genetics and pathogenesis. Annu. Rev. Pathol. 6, 193–222 (2011). Article  CAS  Google Scholar  Sims, R., Hill, M. & Williams, J….

Hi all, I am trying to count the number of reads that map to each gene using FeatureCounts. (RNA-Seq PE, linux) my input; GFF. file generated using Prokka GTF.file generated by NCBI annotation Sorted.bam files generated by bowtie2 and samtools. When I used gtf.file generated by NCBI, featurecounts run without…

Stringtie prepDE.py script 0 Hello, I am trying to generate gene count matrix and transcript count matrix using stringtie-prepDE.py script, I know that it expects input a certain way, I was wondering if it’s possible to provide it a folder (let’s call it ballgown for now) with a bunch of…

“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 . ?…

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

lncRNA analysis tutorial 2 hello, I would like to ask if there is some good tutorial concerning analysis of lncRNA along RNAseq analysis? like practical example. thank you for your help. lncRNA RNA-seq • 458 views Generally speaking, doing differential expression (DE) or transcript discovery on lncRNA is no different…

Software official website ： Hisat2： Manual | HISAT2 StringTie：StringTie article ：Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial ： 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…

Finding DEGs from HISAT2/STRINGTIE output 0 Hello, I have to search for DEGs from four samples of crop. I am following reference based mapping of reads to genome using HISAT2. I have completed till the generation of merged .gtf files for the samples using STRINGTIE. Since I am new to…

Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010). Article  Google Scholar  Guttman, M. et al. Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28,…

Background: The application of RNA-seq technology has become more extensive and the number of analysis procedures available has increased over the past years. Selecting an appropriate workflow has become an important issue for researchers in the field. Methods: In our study, six popular analytical procedures/pipeline were compared using four RNA-seq…

How to extract fasta sequences from assembled transcripts generated by Stringtie 4 Hi all, I used STAR and stringtie for mapping reads to reference genome and assembly. As you know, the generated assembled transcripts by stringtie are in gtf format. Now, I want to have fasta sequence of assembled transcript….

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Name Last modified Size Description Parent Directory   –   SOAPdenovo2.hints.html 2019-05-04 15:52 3.9K   Trimmomatic.hints.html 2019-05-20 13:32 6.3K   Trinity.hints.html 2019-04-23 11:39 2.4K   adaptercheck.hints.html 2021-05-13 12:27 8.0K   adaptercheck.html 2021-05-12 17:45 4.9K   adaptercheck_output.png 2021-05-12 17:17 51K   fastq_pair.hints.html 2019-04-05 13:16 3.4K   gffcompare.hints.html 2018-07-18 14:05 3.2K  …

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data. 0 Hi all, asking for a colleague, I’m looking for human non-poly-A mRNA that would end with a specific pattern ( say CCGCAT ). is it possible to find this in a RNA-SEQ data ? (e.g: www.ncbi.nlm.nih.gov//sra?term=SRR059132…

1. Edmonds, R. L. & Eglitis, A. The role of the Douglas-fir beetle and wood borers in the decomposition of and nutrient release from Douglas-fir logs. Can. J. Res. 19, 853–859 (1989). Article  Google Scholar  2. Hlásny, T. et al. Living with bark beetles: impacts, outlook and management options. In:…

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

Finding differentially expressed lncRNA 0 Hi all, I’m trying to diff. expressed lncRNAs between two groups (of humans). I wanted to use the following pipeline: trimmomatic –> stringtie/cufflinks –> Cuffmerge/stringtie merge –> FEELnc to find lncRNAs. To find diff. expressed transcripts I want to use the following pipeline: trimmomatic –>…