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Tag: tophat2
Tophat2 Error running ‘long_spanning_reads’ on M1 Mac
Tophat2 Error running ‘long_spanning_reads’ on M1 Mac 1 Hi everyone, I am trying to perform Tophat2 based genome alignment (I understand there are alternative tools out there, but for this purpose it needs to be Tophat2), but I keep running into issues at the ‘long_spanning_reads’ stage. I’m new to bioinformatics….
Molecular consequences of PQBP1 deficiency, involved in the X-linked Renpenning syndrome
Kalscheuer VM, Freude K, Musante L, Jensen LR, Yntema HG, Gécz J, et al. Mutations in the polyglutamine binding protein 1 gene cause X-linked mental retardation. Nat Genet. 2003;35:313–5. Article CAS PubMed Google Scholar Lenski C, Abidi F, Meindl A, Gibson A, Platzer M, Kooy F, et al. Novel truncating…
GATK AnnotateVcfWithBamDepth returns zero DP for all variants in VCF
Dear all, I am using GATK (v4.1.9.0) AnnotateVcfWithBamDepth to get the DP for all variants in ClinVar VCF in a retina RNA-seq BAM file. However, the tool returns zero depth for all variants in the VCF, even though I checked multiple variants in IGV and I saw that they are…
Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs | BMC Genomics
Wähner M, Brüssow K. Biological potential of fecundity of sows. Biotechnol Anim Husb. 2009;25(5–6–1):523–33. Article Google Scholar Argente MJ. Chap. 4 Major Components in Limiting Litter Size. In: 2018; 2018. Malopolska MM, Tuz R, Schwarz T, Ekanayake LD, D’Ambrosio J, Ahmadi B, Nowicki J, Tomaszewska E, Grzesiak M, Bartlewski PM….
Dryad | Data — RNAseq data from: Medial prefrontal cortex samples of glutamate dehydrogenase-deficient mice, stress-exposed or -naive, and their Nestin-Cre+ controls
Glutamate abnormalities in the medial prefrontal cortex (mPFC) are associated with cognitive deficits. We previously showed that homozygous deletion of CNS glutamate dehydrogenase 1 (Glud1), a metabolic enzyme critical for glutamate metabolism, leads to schizophrenia-like behavioral abnormalities and increased mPFC glutamate; mice heterozygous for CNS Glud1 deletion (C-Glud1+/- mice) showed…
tophat2 installation error
tophat2 installation error 1 Hi, I am trying to install tophat2 . tried this command conda install -c bioinfo tophat2 but got this error : Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with…
DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies | BMC Bioinformatics
Mertens F, Johansson B, Fioretos T, Mitelman F. The emerging complexity of gene fusions in cancer. Nat Rev Cancer. 2015;15(6):371–81. Article CAS PubMed Google Scholar Peters S, Camidge DR, Shaw AT, Gadgeel S, Ahn JS, Kim DW, et al. Alectinib versus crizotinib in untreated ALK-positive non-small-cell lung cancer. N Engl…
Tophat2 manual pdf | Peatix
Tophat2 manual pdf Rna$ sequencing- data- analysis, – nsci- 580a3, – fall, -! linux_ x86_ 64/ tophat2. ln – s ~ / tophat- 2. qiagen, with its leading expertise in sample preparation technologies, has developed a complete portfolio of dedicated products to optimize your workflow – on any ngs instrument….
Tophat2 Multiple alignment discrepancy – SEQanswers
Dear All, I am trying to get unique sequences when align to hg19 using tophat2. When I set parameter “Maximum number of alignments to be allowed” to 1,I got 25% of my data as “multiple alignment” sequences while I got 58% when I set the parameter to 20. As…
Is it correct to use Tophat2 directly followed by Cuffquant to only align to the reference transcriptomes without wishing to assemble new transcripts?
Is it correct to use Tophat2 directly followed by Cuffquant to only align to the reference transcriptomes without wishing to assemble new transcripts? 1 Hi, friends. I only want to perform differential expression analysis on the annotated transcripts of my existing reference genome. I use tophat2 for alignment with –no-novel-juncs…
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,…
TopHat2 Download URL Broken?
TopHat2 Download URL Broken? 1 $ wget ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz –2021-11-24 18:44:24– ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz Resolving ccb.jhu.edu (ccb.jhu.edu)… 128.220.233.141 Connecting to ccb.jhu.edu (ccb.jhu.edu)|128.220.233.141|:443… connected. OpenSSL: error:1414D172:SSL routines:tls12_check_peer_sigalg:wrong signature type Unable to establish SSL connection. Also their other download links seem to be broken? ccb.jhu.edu/software/tophat/downloads/ Is there a mirror for TopHat2? tophat tophat2 • 57…
The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus
1. Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 281, 237–240 (1998). ADS CAS PubMed Google Scholar 2. Nelson, D. M., Tréguer, P., Brzezinski, M. A., Leynaert, A. & Quéguiner, B. Production and dissolution of…
Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity
1. Hoegh-Guldberg, O. & Bruno, J. F. The impact of climate change on the world’s marine ecosystems. Science 328, 1523–1528 (2010). CAS PubMed Google Scholar 2. Chou, C. et al. Increase in the range between wet and dry season precipitation. Nat. Geosci. 6, 263–267 (2013). CAS Google Scholar 3. Li,…
Diverse alterations associated with resistance to KRAS(G12C) inhibition
1. Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A. & Shokat, K. M. K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature 503, 548–551 (2013). ADS CAS Article Google Scholar 2. Lito, P., Solomon, M., Li, L. S., Hansen, R. & Rosen, N. Allele-specific inhibitors inactivate…
Bioinformatics Scientist – Job at DAWSON in Bethesda, MD
Bioinformatics Scientist Full Time Prof-Entry Bethesda, MD, US DAWSON is a Native Hawaiian Organization 8(a) small business that brings the Spirit of Aloha to our employees. As part of the DAWSON “Ohana”, you will be provided a best-in-class benefits program that strives to ensure our great people have peace of…
Splice sequence indexing failed with err =127
Tophat2 Error: Splice sequence indexing failed with err =127 0 I’ve been trying to map my RNA-seq results onto an entire genome, and I’ve encountered a problem with splices. The script.pbs I submitted to cluster servers is: #PBS -N tophat_cufflinks_1 #PBS -o tophat_cufflinks_1_out.txt #PBS -e tophat_cufflinks_1_error_out.txt #PBS -l nodes=cu01:ppn=24 export…
Bioinformatics Scientist with Security Clearance job in Bethesda at Dawson
Company Description Dawson is a Staffing & Recruiting agency that was founded in 1946 and headquartered in Columbus, OH. They have the vision to help the small as well as large corporations and businesses to recruit the talent that can help them to provide the best customer service with exceptional…
bowtie2 and then HISAT2? What does it mean in Data processing details on a paper?
bowtie2 and then HISAT2? What does it mean in Data processing details on a paper? 1 IMHO that must be a mistake: the data seems to be RNA so I would’ve directly gone for TopHat2 (or HISAT2). (Unless they wanted to run Fastqc in BAM, not fastq mode – in…
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Hi all, I am a PhD student with biology background. I recently inherit a RNA Sequencing project from another PhD student in my lab. We already have paired-ended RNA-Seq data generated from Illumina HiSeq but haven’t started analysis yet. I have basic Linux command line training but have no idea about how…
Fastqc user manual – vodosp.ru
FASTQ format – Wikipedia 06 September 2021 – by TC Collin · 2020 · Cited by 3 — Be accompanied by a step-by-step user-friendly manual, If the user performs FastQC prior to the removal of adapters (step 3), the length Both programs can be used on Linux/MacOS X machines and quite…
IOError [errno 2] No such file or directory: ‘-o’
TopHat error: IOError [errno 2] No such file or directory: ‘-o’ 2 Hello everyone. I’m now running tophat in our server. First, I just simply tried “tophat -p 8 -G <gtf_file> <ref_genome> <fa1><fa2>” and it worked. Then I wrote a for loop scripts but It reported error: [2019-04-03 10:49:16] Beginning…
Spliiting the bam files into separate samples ,tophat2
Spliiting the bam files into separate samples ,tophat2 0 Hi everyone, I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files…