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 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[……] […] 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[……] […] 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[……] […] 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/Junior快5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[……] […] 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[……] […] 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[……] […] 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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