Hello Bao,
Trimming is a different operation than removing sequences and could be applied to both RNA and DNA data. Unfortunately, there are no generalized rules that could be applied to all cases.
The type of data and the mapping tool will determine if trimming is needed and when it should be done.
Some mappers have quality trimming options in the tool form itself (for example, Bowtie, in the full parameter list).
These screencasts may help, as would the target mapping tool documentation.
http://wiki.g2.bx.psu.edu/Learn/Screencasts see: Basic FASTQ Manipulation Advanced FASTQ Manipulation
For next time, please continue to send questions with the "to" address as the mailing list and replies as "reply-all, it helps us greatly with tracking.
If anyone else on the mailing list has more help to offer, they are welcome to jump in on the discussion. Although, you would likely need to post to the mailing list the source/format of your query data and which tool you are considering using in order to receive specific advice.
Best,
Jen Galaxy team
On 2/16/12 8:20 AM, vang0280@umn.edu wrote:
Dear Jennifer,
That was very helpful!
Would this also apply to trimming reads that have a low median or bottom quartile score as well for RNA Seq data? Would you recommend for Tophat vs Bowtie vs BWA?
If not when would you trim reads when wouldn't you trim your reads?
Thanks
Bao
On Feb 15 2012, Jennifer Jackson wrote:
Hello Bao,
For RNA-seq analysis, removing any reads would be problematic since this would interfere with expression/abundance calculations. For mapping, TopHat is the preferred alignment tool for spliced RNA data. BWA and Bowtie are tools better suited for DNA mapping.
For Prokaryote genomes, the choice of which alignment tool to use may be more flexible (splicing would not be an issue), but understanding the parameters for the tool options and how to tune appropriately (e.g. for a circular genome) would be important to research and test out.
For more details about TopHat, please see the author's web site (including an FAQ) at: http://tophat.cbcb.umd.edu/. A help email is also available: tophat.cufflinks@gmail.com.
Best,
Jen Galaxy team
On 2/15/12 9:39 AM, vang0280@umn.edu wrote:
Dear all,
When is it necessary to remove duplicate reads from your RNA Seq analysis?
Is it required for Tophat versus BWA versus Bowtie?
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