Re: [galaxy-user] cufflinks FPKM problem

2011-04-11 Thread Paul Korir
Hi Li, Tophat includes a custom tag 'XS' at the end of spliced read alignments which your pipeline is not aware about. The following is taken from http://cufflinks.cbcb.umd.edu/manual.html Cufflinks takes a text file of SAM alignments as input. For more details on the SAM format, see the

Re: [galaxy-user] cufflinks FPKM problem

2011-04-11 Thread Ryan Golhar
Cufflinks requires an 'xs' tag on each read in the bam file. Only tophat does this. You can write a script to add this or remap with tophat. How much of a difference do you see between tophat and bioscope? Please excuse any typos -- Sent from my iPhone On Apr 11, 2011, at 9:46 AM, lishiyong

Re: [galaxy-user] cufflinks FPKM problem

2011-04-11 Thread Adam Roberts
23:19:10 *收件人：* lishiyong *抄送：* tophat.cufflinks; galaxy-user; 高欢 *主题：* Re: [galaxy-user] cufflinks FPKM problem Cufflinks requires an 'xs' tag on each read in the bam file. Only tophat does this. You can write a script to add this or remap with tophat. How much of a difference do you see

Re: [galaxy-user] cufflinks FPKM problem

2011-04-11 Thread gaohuan
： tophat.cufflinks; galaxy-user; 高欢 主题： Re: [galaxy-user] cufflinks FPKM problem Cufflinks requires an 'xs' tag on each read in the bam file. Only tophat does this. You can write a script to add this or remap with tophat. How much of a difference do you see between tophat and bioscope

Re: [galaxy-user] cufflinks FPKM problem

2011-04-11 Thread 李世勇
]）:+ ? Best wishes - 原始邮件 - 发件人: Paul Korir polaris...@gmail.com 收件人: lishiyong lishiy...@genomics.org.cn 抄送: tophat.cufflinks tophat.cuffli...@gmail.com, galaxy-user galaxy-user@lists.bx.psu.edu, 高欢 gaoh...@genomics.org.cn 发送时间: 星期一, 2011年 4 月 11日 下午 11:10:56 主题: Re: [galaxy-user] cufflinks FPKM