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• • Neel@neelam

  

  Neel posted to the wire 2254 days ago

  Understanding Alignments https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session5-alignedReads.html #Understanding #Alignments
• • Neel@neelam

  

  Neel bookmarked BamView: a free interactive display of read alignments in BAM data files 2254 days ago

  To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the command line with the...

  http://bamview.sourceforge.net/
• • Neel@neelam

  

  Neel created a new bio-script CollectGcBiasMetrics.jar will generate a GC bias plot for each contig 2254 days ago
• • Neel@neelam

  

  Neel bookmarked AMStat: display statistics of large sequence files from next generation sequencing projects 2254 days ago

  SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...

  http://samstat.sourceforge.net/
• • Neel@neelam

  

  Neel bookmarked pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks 2254 days ago

  pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig bed (many options) bedgraph links (represented as arcs) Hi-C matrices (if HiCExplorer is...

  https://github.com/deeptools/pyGenomeTracks
• • Neel@neelam

  

  Neel created a new bio-script Script to Plot the Coverage 2254 days ago
• • Neel@neelam

  

  Neel created a new bio-script Collecting arguments with R 2254 days ago
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh posted to the wire 2257 days ago

  Louvain algorithm https://neo4j.com/docs/graph-algorithms/current/algorithms/louvain/ #Louvain #algorithm
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2258 days ago

  Long reads: their purpose and place https://academic.oup.com/hmg/article/27/R2/R234/4996216 #Long #reads #informations
• • Neel@neelam

  

  Neel bookmarked MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other... 2259 days ago

  An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to...

  https://github.com/olarerin/metaPlotR
• • Jit@jit.aber

  

  Jit bookmarked Referee: Genome assembly quality scores 2259 days ago

  Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...

  https://gwct.github.io/referee/#
• • Rahul Nayak@rahul

  

  Rahul Nayak published a news post Illumina to Acquire Pacific Biosciences for Approximately $1.2 Billion ! 2261 days ago

  https://www.illumina.com/company/news-center/press-releases/2018/2374913.html
• • Jit@jit.aber

  

  Jit posted to the wire 2261 days ago

  Rename the fasta header perl -ane 'if(/\>/){$a++;print ">LR$a\n"}else{print;}' allPacBio_clean.fa > allPacBio_clean_shortName.fa #fasta #header #rename
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life 2262 days ago

   Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...

  http://ancestralgenomes.org/
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked swgis v2.0 : a seqword genomic island sniffer 2262 days ago

  swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages....

  http://eugi.bi.up.ac.za/eugi_download_swgis.php
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 2262 days ago

  The Open Bioinformatics Journal https://www.benthamopen.com/TOBIOIJ/ #Note impact factor ~4 ... ??? 
• • Neel@neelam

  

  Neel posted to the wire 2264 days ago

  Bioinformatics jobs at CUJ, Jharkhand http://www.cuj.ac.in/downloads/advtbuilderDLS25oct2018.pdf #Job
• • Jit@jit.aber

  

  Jit commented on a page titled Tools for Searching Repeats And Palindromic Sequences 2264 days ago

  I wrote a tools "Palindromer" to find palindromes in whole genome sequences. You can try https://github.com/jnarayan81/Palindromer . I am happy to improve it, if any features are requested. 
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh commented on a bookmark PhenoGram 2264 days ago

  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015356/
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh commented on the blog Tools to detect synteny blocks regions among multiple genomes 2264 days ago

  It is recommended to used genomes (N50 > 1Mb) for synteny analysis https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2026-4

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