gff3 to gft method

The easiest way is to use the gffread program that comes with the Cufflinks software suite (Tuxedo) gffread my.gff3 -T -o my.gtf See gffread -h for more information

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KEGG annotation pipeline

KEGG Pathway Pipeline: blastall -p blastp -d KEGG -i Haiyan.Pep.fasta -m 7 -a 10 -o Haiyan.Pep.fasta.blastp.m7 & ./tBLASTnParser.pl Haiyan.Pep.fasta.blastp.m7 Haiyan.Pep.fasta.blastp.m8 sed ‘1,1d’ Haiyan.Pep.fasta.blastp.m8 > Haiyan.Pep.fasta.blastp.m8.delhead /home/zhouzh/lib/454-2.5/bin/ru[……]

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Reordering contigs in draft genomes by MAUVE

When to use Mauve Contig Mover (MCM)

The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome.  The functionality of this software module has been described in Rissman et al. 2009 , a publication in Bioinformatics. The Mauve Contig Mover can ease a com[……]

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PyroHMMvar: a sensitive and accurate method to call short INDELs and SNPs for Ion Torrent and 454 data

Motivation: The identification of short indels and SNPs from Ion Torrent and 454 reads is a challenging problem, essentially because these techniques are prone to sequence erroneously at homopolymers and can, therefore, raise indels in reads. Most of the existing mapping programs do not model homopo[……]

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微生物基因组中的GC-skew(zhuantie)

如果给出两个关键词:生物信息、GC,可能很多人的第一反应是“GC含量”(GC-content)或者“CpG岛”(CpG island)吧。这两个星期开始做非编码RNA(Non-coding RNA)预测(对象是Sinorhizobium meliloti,草木樨中华根瘤菌),接触到一个以前没听说过的新的“GC理论”:GC-skew.查国内文献,几乎找不到对它的详细介绍(也没有对应的中文翻译,skew有“ 歪,偏, 斜”的意思,通过我对这个理论的理解,就把GC-skew翻译为“GC偏移”吧)。这里翻译一篇Nature上的Review,和大家分享一下。                  [……]

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Solexa与Hiseq测序技术中常见术语名词解释

Hiseq测序技术名词解释 第二代测序技术中Solexa以及它的升级版Hiseq,目前使用最多。为了帮助PLoB网友进一步了解Solexa相关的概念。与大家分享一篇网上看到的文章《Solexa测序技术中常见术语解释》,文章后面有参考来源链接。更多相关信息欢迎加入PLoB 2000人的生物信息QQ群(群号:235461986)来讨论,有相关测序以及生物信息学问题需要解答欢迎前来。下面直接附上相关的解释。大家同时可以结合上面的示意图,了解SolexaHiseq的基本结构。 SBS:边合成边测序反应,每次SBS会延伸一个碱基,大约耗时70分钟。 Run:单次上机测序反应,可以产生4G-75G测序通量不等。[……]

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Illumina MiSeq 与GS FLX/Junior、Ion Torrent PGM性能比较

Illumina MiSeq 与GS FLX/Junior性能比较表

   

Illumina MiSeq

GS FLX/Junior

实验流程和周期 提供最快的二代测序的实验流程, 可在8小时内完成从DNA样本其实到分析后的数据,比GS FLX/Junior5倍。流程包括:l   文库制备:1.5小时,使用快速、transposon-based Nextera方法 l   在一个仪器系统内、以不到4.5小时(1 X 36 bp)的时间完成从自动话的簇生成到测序 l   在同一个仪器系统内,以不到2小时的时间完成初级和次级测[……]

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RazerS 3: Faster, fully sensitive read mapping

Motivation: During the last years NGS sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is cruc[……]

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Qualimap: evaluating next generation sequencing alignment data

Motivation: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often[……]

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第三代测序技术

如果有人告诉你用显微镜实时观测单分子DNA聚合酶复制DNA,并用它来测序,你一定会 认为他异想天开,没有一点生物的sense。 我最初就是这样认为的,然而它不仅可以实现,而且已经实现了!这个就是被称为第三 代的测序技术,Pacific Biosciences公司推出的“Single Molecule Real Time (SMRT ™) DNA Sequencing”(单分子实时DNA测序)。 我有幸在NIH听到了这个技术发明人Stephen Turner博士的讲座,根据自己粗浅的理解 记录整理一下。 要实现单分子实时测序,有三个关键的技术。 第一个是荧[……]

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