Tag: tophat2

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…

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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…

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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,…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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