Categories
Tag: StringTie
My paired end data became single end data after mapping
My paired end data became single end data after mapping 1 Dear community, Something weird happened to me, my public dataset is obviously paired-end data (stated in ‘metadata’ part of ENA database, and there are two seperate fastq files (R1 & R2) and index file (I1) per sequencing run). After…
LncRNA pipeline
Forum:LncRNA pipeline 0 HI ALL, I AM WORKING ON FINDING LNCRNA, I WOULD LIKE TO CHECK IF MY PIPELINE IS RIGHT FIRST I MAP USING STAR AND THEN SORT IT AND THEN GO FOR HTSEQ -GET THE COUNT DATA AND DO DESEQ. FOR LNCRNA EXTRACTION FROM RNA SEQ, I AM…
How to setup the pipeline of the RNA-Seq FASTQ file processing (macOS version)
This is a guide for preparing for importing RNA-Seq FASTQ files to Subio Platform on a Mac computer. If you use a Windows10 machine, please go to the guide for Windows10. Subio Platform utilizes the following tools to process the RNA-Seq FASTQ files. fastp to trim adapters and filter low-quality…
Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)
Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….
Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica
Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…
overlapping duplicate dispersed_repeat feature in stringtie
GFF Error: overlapping duplicate dispersed_repeat feature in stringtie 0 Hi. I got following error when I use stringtie. with repeatmasker annotation gff file and RNA-seq bam files which is already sorted with samtools. GFF Error: overlapping duplicate dispersed_repeat feature (ID=461) GFF Error: overlapping duplicate dispersed_repeat feature (ID=712) GFF Error: overlapping…
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder 0 Hi all, I am running a workflow to identify single copy orthogroups from RNAseq data including 9 species in a family of non-model organisms. All 9 species are closely related enough that they can be aligned to…
Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish
Krause, J. & Ruxton, G. D. Living in Groups (Oxford Univ. Press, 2002). Réale, D., Reader, S. M., Sol, D., McDougall, P. T. & Dingemanse, N. J. Integrating animal temperament within ecology and evolution. Biol. Rev. 82, 291–318 (2007). Article PubMed Google Scholar Gartland, L. A., Firth, J. A., Laskowski,…
DESeq2 design with unbalance data and a multifactor design
Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…
DESeq2 with unbalanced dataset and multifactor design
Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…
Comparative transcriptomics between species
Comparative transcriptomics between species 0 Hey all, I am new to the transcriptomics world, therefore I have some questions. I am currently working on a study where the goal is to compare transcriptomes across 5 species. I mapped all rna-seq to reference genomes (different for every species) using Hisat2, then…
Transcript count normalization using Deseq2
Transcript count normalization using Deseq2 0 Hi, I need to look for difference’s in expression of two different transcripts from the same gene across three different stages of disease. Ie two different comparisons a) comparing expression of these two transcripts b) comparisons across different stages of disease To do this…
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Compagno, L. J. V. Alternative life-history styles of cartilaginous fishes in time and space. Environ. Biol. Fishes 28, 33–75 (1990). Article Google Scholar Kriwet, J., Witzmann, F., Klug, S. & Heidtke, U. H. J. First direct evidence of a vertebrate three-level trophic chain in the fossil record. Proc. Biol. Sci….
Hisat2-build (5.ht2 and 6.ht2 are missing)
Hisat2-build (5.ht2 and 6.ht2 are missing) 0 Hi all, I am trying to index the reference.fasta file using hisat2/stringtie. First I want to index the genome using hisat2. (>hisat2-build ref.fa ref) The manual states that 8 files should be produced after indexing 1.ht2 to 8.h2t. However, I only have six…
file conversion from gtf to gff3 for evidence modeler
file conversion from gtf to gff3 for evidence modeler 0 Hi, could you please guide me how to convert the stringtie output file stringtie_transcript.gtf into .gff3 format for the evidence modeler of genome annotation. gff3 stringtie gtf • 162 views • link updated 32 minutes ago by Ram 41k •…
Stringtie coverage calculation for DE analysis
Stringtie coverage calculation for DE analysis 0 Hello Biostars, I have a question about stringtie and how it assigns reads to a specific transcript isoform. I wanted to perform a Differential Expression analysis using a genome assembly without a gene annotation, as a reference. To do this I have aligned…
TPM from STAR output without re-allign the file using RSEM or Salmon
Hi, I want to get the TPM files from aligned files generate with STAR and reading I found out that the easiest way is using RSEM or Salmon. My code for the alignment is /Users/c/STAR/bin/MacOSX_x86_64/STAR runThreadN 4 –genomeDir /Users/c/Desktop/Human_genome_index –readFilesIn /Users/c/Desktop/test/C1D20_R1_001_paired.fastq /Users/c/Desktop/test/C1D20_R2_001_paired.fastq –quantMode TranscriptomeSAM GeneCounts –outFileNamePrefix C1D20 –outSAMtype BAM SortedByCoordinate…
gffread outputs empty gtf file
gffread outputs empty gtf file 1 Hi, I’ve been trying to convert my prokka output in gff format to gtf format to be able to use for my hisat-stringtie analysis. However, using gffreads to convert yields an empty gtf file. Im not sure if im going wrong somewhere. Any help…
quantifying splicing transcripts for nanopore RNAseq
quantifying splicing transcripts for nanopore RNAseq 0 Hi all, I’m looking for some help in quantifying the number of transcripts in a virus genome from nanopore RNAseq data. I’ve currently been mapping the RNAseq data back to the reference genome using minimap, and then running Nanosplicer and stringtie to quantify…
Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism
Harley, R. M. et al. Labiatae. in Flowering Plants · Dicotyledons. The Families and Genera of Vascular Plants (ed. Kadereit, J. W.) vol. 7 167–275 (2004). Kokkini, S., Karousou, R. & Hanlidou, E. HERBS | Herbs of the Labiatae. Encyclopedia of Food Sciences and Nutrition 3082–3090 (2003) doi.org/10.1016/B0-12-227055-X/00593-9. Hao, D….
Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…
How to convert original BED file to a GTF ?
How to convert original BED file to a GTF ? 1 Hello everyone, Now, I use Linux base for analyse HISAT2, Stringtie, ballgown. I have the original BED file and I would like to convert to GTF file for Stringtie analysis. If you have some suggestion about tool Or command…
class codes x , lncRNA
class codes x , lncRNA 0 can anyone help me from getting class codes X from lnc rna filtering. i am getting very less transcripts of class codes x. is there anything to do with the stringtie or cuffcompare options inorder to get class codes x. tq codes X lncRNA…
Dynamic RNA profiles in the small intestinal epithelia of cats after Toxoplasma gondii infection | Infectious Diseases of Poverty
Jacobs L. Toxoplasma and toxoplasmosis. Annu Rev Microbiol. 1963;17:429–50. Article CAS PubMed Google Scholar Montoya JG, Liesenfeld O. Toxoplasmosis. The Lancet. 2004;363(9425):1965–76. Article CAS Google Scholar Dubey JP. Duration of immunity to shedding of Toxoplasma gondii oocysts by cats. J Parasitol. 1995;81(3):410–5. Article CAS PubMed Google Scholar Dubey JP, Frenkel…
Single end RNAseq data strandedness infer-experiment-py
Single end RNAseq data strandedness infer-experiment-py 2 Hi all, I have a single end RNAseq data and would like to understand the strandedness of the data. From wet-lab input I know “Stranded cDNA library was generated by reverse transcribing the RNA molecules”. I used infer-experiment-py The output is: This is…
Understand GTF produced by StringTie
Understand GTF produced by StringTie 0 Hi, I’m collaborating in a project where the transcriptome of Arabidopsis thaliana was assembled with StringTie. Since the aim of the project is also to look into the long-non-coding RNA transcripts, just a few of them were kept. I need to retrieve the correspondence…
Stringtie problem
Stringtie problem 0 I have found a problem while doing the part of estimation using stringtie technique, I work on TB bacterium genome and its Gff file ( I only found annotation file in gff on ensemble) , it gives me an erro that tells” can not find gene ID…
How to to lncRNA analysis from WTS data ?
How to to lncRNA analysis from WTS data ? 0 Hi, I have WTS data with me and I have to do mRNA analysis, lncRNA analysis etc. using the data. Until now what I have done is map the pre-processed data to reference genome using Hisat2 and do quantification using…
IsoformSwitchAnalyserR lmportR data warning.
I am trying to run IsoformSwitchAnalyzeR using R version 4.3.0 using following command: aSwitchList2 <- importRdata( isoformCountMatrix = salmonQuant$counts, isoformRepExpression = salmonQuant$abundance, designMatrix = myDesign, isoformExonAnnoation = “gencode.v40.annotation.gtf.gz”, isoformNtFasta = “gencode.v40.transcripts.fa”, addAnnotatedORFs = TRUE, showProgress = TRUE, ignoreAfterBar =FALSE) This is the Output : Step 1 of 10: Checking data…Step…
The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes
Purohit, J., Kumar, A., Hynniewta, M. & Satyawada, R. R. Karyomorphological studies in guar (Cyamopsis tetragonoloba (Linn.) Taub.)—An important gum yielding plant of Rajasthan, India. Cytologia 76(2), 163–169 (2011). Article Google Scholar Gillett, J. B. Indigofera (Microcharis) in tropical Africa with the related genera Cyamopsis and Rhynchotropis. H.M.S.O Kew Bull.,…
ChatGPT optimized for bioinformatics questions
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
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…
The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
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…
pacbio – StringTie discovers less novel isoforms when reference annotation is provided
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…
Index of /Atumefaciens/20230426-pgen-HISAT2-stringtie-gffcompare-RNAseq/heart
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
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
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
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
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
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…
How to run prepDE.py3?
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
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
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?
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
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
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…
Identification and characterization of CircRNA-associated CeRNA networks in moso bamboo under nitrogen stress | BMC Plant Biology
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
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
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…
Cas9-mediated replacement of expanded CAG repeats in a pig model of Huntington’s disease
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….
PROKKA.gff file is not compatible with featureCounts
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
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
“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 . ?…
Evolution of stickleback spines through independent cis-regulatory changes at HOXDB
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
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…
Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq
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
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…
Accurate assembly of multi-end RNA-seq data with Scallop2
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,…
A comparison of transcriptome analysis methods with reference genome
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
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….
HRJOB7442 Bioinformatics Scientist 2 (Various Locations) in Nether Alderley, Macclesfield (SK10) | Almac Group (Uk) Ltd
Bioinformatics Scientist 2 Hours: 37.5 hours per week Salary: Competitive Ref No: HRJOB7442 Business Unit: Diagnostic Services Location: Craigavon or Manchester Open To: Internal and External Applicants The Company Almac Diagnostic Services is a leading stratified medicine business, specialising in biomarker-driven clinical trials. We are incredibly proud to be involved…
Index of /~psgendb/doc/bioLegato/blreads
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 …
iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data
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.
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…
A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest
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
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
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
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 –>…