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• • Jit@jit.aber

  

  Jit bookmarked GeneOverlap: An R package to test and visualize gene overlaps 2206 days ago

  Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose,...

  https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf
• • Jit@jit.aber

  

  Jit commented on a page titled Perl one-liner for bioinformatician !!! in the group Perl *PIPERs 2206 days ago

  This tutorial is useful https://blogs.oracle.com/linux/the-top-10-tricks-of-perl-one-liners-v2
• • Jit@jit.aber

  

  Jit bookmarked NanoPack: visualizing and processing long-read sequencing data 2208 days ago

  The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...

  https://github.com/wdecoster/nanopack
• • Jit@jit.aber

  

  Jit created a new bio-script Split the multifasta in separate files ! 2208 days ago
• • Neel@neelam

  

  Neel commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 2210 days ago

  Cells accept bioinformatics papers https://www.mdpi.com/journal/cells/special_issues/bioinformatics_cells
• • BioStar@biostar

  

  BioStar commented on a page titled Bioinformatics Companies in India 2211 days ago

  quantumzyme in india http://quantumzyme.com/
• • Jit@jit.aber

  

  Jit bookmarked Versatile genome assembly evaluation with QUAST-LG 2212 days ago

  QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST  package starting from version 5.0.0 (download the latest release). Run QUAST as...

  http://cab.spbu.ru/software/quast-lg/
• • Jit@jit.aber

  

  Jit posted to the wire 2212 days ago

  Is It #Ordered Correctly? #Validating #Genome #Assemblies by Optical Mapping http://www.plantcell.org/content/30/1/7
• • Rahul Nayak@rahul

  

  Rahul Nayak commented on the file Assembly tutorial PPT 2212 days ago

  Genome assembly tutorial https://astrobiomike.github.io/genomics/de_novo_assembly
• • Neel@neelam

  

  Neel commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 2213 days ago

  Nucleus journal accept bioinformatics tool and software papers https://www.springer.com/life+sciences/cell+biology/journal/13237
• • Shruti Paniwala@shruti

  

  Shruti Paniwala bookmarked Genome Annotation using MAKER tutorial ! 2213 days ago

  MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite...

  https://www.biostars.org/p/261203/
• • Shruti Paniwala@shruti

  

  Shruti Paniwala posted to the wire 2213 days ago

  Gene prediction tools http://genome.crg.es/courses/laCaixa05/Prediction/index.html #Genes #Predicts
• • Jit@jit.aber

  

  Jit posted to the wire 2213 days ago

  Export the PATH in Linux $ PATH="/home/urbe/Tools/ALLHiC/scripts:${PATH}" and then $ export PATH #Path #Set #Variable
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2213 days ago

  Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count
• • BioStar@biostar

  

  BioStar bookmarked ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data 2213 days ago

  The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed...

  https://github.com/tangerzhang/ALLHiC/wiki
• • BioStar@biostar

  

  BioStar posted to the wire 2213 days ago

  Blast database https://ftp.ncbi.nih.gov/blast/db/ #blast #database
• • BioStar@biostar

  

  BioStar bookmarked FGENESH - Program for predicting multiple genes in genomic DNA sequences 2213 days ago

  FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et...

  http://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind
• • Jit@jit.aber

  

  Jit posted to the wire 2215 days ago

  #Split the #BAM file $ /home/urbe/Tools/bamtools/bin/bamtools split -in improved3.fasta.sorted.bam -reference #bamtools
• • Jit@jit.aber

  

  Jit posted to the wire 2216 days ago

  Extract sequence by ids $ xargs samtools faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa #Extract #Ids #Sequences
• • Jit@jit.aber

  

  Jit bookmarked Biotite: A general framework for computational biology 2216 days ago

  The package is open source and freely available at GitHub (https://github.com/biotite-dev/biotite). This package is simple to use especially for the beginners in programming and computationally efficient because of the implementation of Numpy and...

  https://github.com/biotite-dev/biotite

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