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Structure of Binary files used for storing sequencing data-bam and sff
...bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less spa...ho looking for structure of Bam and sff file: Bam: http://samtools.sourc...mats&m=doc&s=format#sff Binary file Editor and Viewer: http://mh...3922 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...oinformatics 25(16):2078-9, 2009 PubMedCentral SAM format specification file Efficient storage of high th...nd answers on bioinformatics and computational genomics. Information on file formats used by the Universit...3782 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
...ckage is written in C and is available as a tar file. http://www.broadinstitute.or...quence evolution http://bit.ly/rlsim-gitpIRS Profile-based Illumina pair-end reads...kage simulating the evolution of copy number profiles along a tree. http://bit.ly/...3740 days ago
List of In-silico Binding Site Prediction Tools
...ed a database called sc-PDB. The sc-PDB database provides separated MOL2 files for the ligand, its binding...calculate pore dimensions and analyze atom accessibility. MolAxis reads files in the standard Protein Data...3747 days ago
Linux for bioinformatician !!!
...cian plesae read this article "An introduction to Linux for bioinformatics" by Paul Stothard. Linux cheat sheet at http://bioinformaticsonline.com/file/view/87/linux-cheat-sheet Pl...3708 days ago
Perl one-liner for bioinformatician !!!
...lines, parsing logs, editing files in-place, doing statistics,...' #double space a fileperl -pe '$_ .= "\n" unless /^...umber of non-empty lines in a fileperl -lne '$a++ if /regex/; EN...05/split-multi-fasta-sequence-file/3631 days ago
Next generation sequencing in R or bioconductor environment
...ace for exporting annotation feature data to various genome browsers and file formats (such as GFF). See th...uch a count table can be imported into R or generated from BAM alignment files using the countOverlaps func...3627 days ago
Commercial and public next-gen-seq (NGS) software
...r, 454, ilumina), parse caf, ace and bowtie map files, clean and filter contigs, l...uence Analyzer output that uses the probability files instead of the sequence file...e Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH. Perl...3521 days ago
- Subprocess is one of simplest way of running linux command from within python code Example: if you want to run fastqc for QC of fastq file: from subprocess import Popen,PIPE,call...
3552 days ago
Apps for Busy Bioinformatics Researchers !!!
...ing and analysis of DNA sequencing files - ab1. It includes handy too...ine the quality of your sequencing files. This app works with cloud...ing and analysis of DNA sequencing files - ab1. It includes handy too...o gene info on websites. Download files for offline use. (.pdf, .mp3...3544 days ago
