Re: [galaxy-user] about Mapping Quality

2012-02-08 Thread Kevin Silverstein
-user@lists.bx.psu.edu" Subject: Re: [galaxy-user] about Mapping Quality Message-ID: <84af17b7-3317-43cf-92ba-c60d17a6e...@emory.edu> Content-Type: text/plain; charset="us-ascii" Tophat/Bowtie does not yield mapping quality, so, as per the SAM spec, that field is set to

Re: [galaxy-user] about Mapping Quality

2012-02-07 Thread Jeremy Goecks
Tophat/Bowtie does not yield mapping quality, so, as per the SAM spec, that field is set to 255, indicating that quality is unavailable. http://samtools.sourceforge.net/SAM1.pdf Best, J. On Feb 7, 2012, at 5:46 PM, Li, Jilong (MU-Student) wrote: > Hi all, > > I used TopHat to map RNA-Seq read

[galaxy-user] about Mapping Quality

2012-02-07 Thread Li, Jilong (MU-Student)
Hi all, I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the value of some mapping quality (the 5th column) is 255. What does it mean? And I found these reads which have mapping quality 255 mapped to unique place. Thanks! Victor