bedtools: a powerful toolset for genome arithmetic — bedtools 2.31.0 documentation
bedtools: a powerful toolset for genome arithmetic¶ Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic
ALLPATHS-LG | High quality genome assembly from low cost data
We are pleased to announce the release of DISCOVAR de novo, our new assembler that is suitable suitable for large genomes up to human size. DISCOVAR de novo, uses the same cheap data that the original DISCOVAR release does: 250 base paired-end PCR-free Illumina reads. No other libraries are required. For more information please visit the DISCOVAR blog, or check out the online demo.
HTS mappers
About This page attempts to provide an up-to-date compendium of HTS mappers initially provided in the article "Tools for mapping high-throughput sequencing data", Bioinformatics (2012) 28 (24): 3169-3177. Any suggestions are welcome. If your mapper is not listed or you want to update the data for your mapper then please let us know by filling this form and we will update the list. Mappers Timeline
Stampy — Wellcome Centre for Human Genetics
Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from
Variant calling using SAMtools - Bioinformatics Team (BioITeam) at the University of Texas - UT Austin Wikis
We are going to conduct the variant calling exercises in an interactive idev session just so you can get a feel for this mode of computing. Almost everything you see here can easily be bundled up into batch scripts and run in that mode. Introduction Variant calling, at first glance, is pretty simple: Map sequence reads to an appropriate reference, emitting BAM files; Generate pileups and look for
Perl and SAM - Dave Tang's blog
Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. If you are having trouble installing Bio::DB::Sam, you may have to recompile SAMTools with the following command: make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC To install the Perl module on a machine where you don't have root access, follow these instructions. Using this module, I recreated the al
BamUtil: bam2FastQ - Genome Analysis Wiki
Overview of the bam2FastQ function of bamUtil The bam2FastQ option on the bamUtil converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files NOTE: Secondary and Supplementary reads are skipped when converting to FastQ. It assumes that there will only be 2 rea
NGS Surfer's Wiki | DEGseqチュートリアル
結果のイメージ 自動生成レポートのイメージ タブ区切りテキストを加工したExcel表 2サンプル間の発現量で有意差のあったものだけ"TRUE"になります。 加工方法はこちら エクセルシートの右端のリンクから、UCSC Genome Browserを起動できます。 エクセルシートでサンプル間で有意だったもののリンクを開いた例 プロット中の赤い点がDEGseqで選択可能な検定手法の一つである"FET:Fisher's Exact Test"で有意とみなされた遺伝子です。少なくとも、Technical replicateでは、有意とみなされる遺伝子が殆どないことから、このシーケンシングプラットフォームによるRNA-Seqの発現変動の検出の再現性が高いことが推察されます。 注：DEGseq内の関数では、標準でRPKM値でなく、タグカウント(遺伝子長で補正をかける前の遺伝子領域に張り付いたタグ数)を
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genomecov — bedtools 2.31.0 documentation
ALLPATHS-LGで使用できるライブラリサイズの制限 - Wolfeyes Bioinformatics beta
Cufflinks, BAM header problem solved... for the moment - SEQanswers
pysam - An interface for reading and writing SAM files — pysam v0.7 documentation
Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events
http://ged.msu.edu/angus/tutorials-2011/index.html
maps: programs for mapping Illumina sequencer reads
pileup formatからmultiple alignment形式を得る
Homer Software and Data Download
Google Code Archive - Long-term storage for Google Code Project Hosting.
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
http://r.livedocs.net/bioconductor/degseq.html