Hello, I am getting what seems to me to be strange results using two different mapping tools in Galaxy. I am mapping illumina RNA-seq data and with tophat, while setting # alignments to 1, I get around 15-20% reads mapping. And when I use bwa, I am getting around 75% reads mapping. My reference is a collection of ESTs so the strength of tophat being a spliced read mapper is probably not being utilized, but I am surprised by the difference in the number of reads mapping between the two. Any thoughts? Austin
Though Tophat calls in Bowtie but they are different mapping tools. Details can be found in mannual of Tophat. For RNA-seq one may be stick with Tophat. Vasu --- On Wed, 4/27/11, Austin Paul <austinpa@usc.edu> wrote: From: Austin Paul <austinpa@usc.edu> Subject: [galaxy-user] mapping with tophat vs. bwa To: galaxy-user@lists.bx.psu.edu Date: Wednesday, April 27, 2011, 4:20 PM Hello, I am getting what seems to me to be strange results using two different mapping tools in Galaxy. I am mapping illumina RNA-seq data and with tophat, while setting # alignments to 1, I get around 15-20% reads mapping. And when I use bwa, I am getting around 75% reads mapping. My reference is a collection of ESTs so the strength of tophat being a spliced read mapper is probably not being utilized, but I am surprised by the difference in the number of reads mapping between the two. Any thoughts? Austin -----Inline Attachment Follows----- ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Hi Vasu, Thanks for your response. I realize tophat and bowtie are different. But my question was concerning what seemed to me to be divergent results from mapping with tophat and bwa (which I also realize are different). bwa seemed to map around 4x the reads that tophat mapped using the same reference. Should this not come as a surprise? Austin On Wed, Apr 27, 2011 at 2:30 PM, vasu punj <punjv@yahoo.com> wrote:
Though Tophat calls in Bowtie but they are different mapping tools. Details can be found in mannual of Tophat. For RNA-seq one may be stick with Tophat.
Vasu
--- On *Wed, 4/27/11, Austin Paul <austinpa@usc.edu>* wrote:
From: Austin Paul <austinpa@usc.edu> Subject: [galaxy-user] mapping with tophat vs. bwa To: galaxy-user@lists.bx.psu.edu Date: Wednesday, April 27, 2011, 4:20 PM
Hello,
I am getting what seems to me to be strange results using two different mapping tools in Galaxy. I am mapping illumina RNA-seq data and with tophat, while setting # alignments to 1, I get around 15-20% reads mapping. And when I use bwa, I am getting around 75% reads mapping. My reference is a collection of ESTs so the strength of tophat being a spliced read mapper is probably not being utilized, but I am surprised by the difference in the number of reads mapping between the two. Any thoughts?
Austin
-----Inline Attachment Follows-----
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Hi Vasu,
Thanks for your response. I realize tophat and bowtie are different. But my question was concerning what seemed to me to be divergent results from mapping with tophat and bwa (which I also realize are different). bwa seemed to map around 4x the reads that tophat mapped using the same reference. Should this not come as a surprise?
Austin
On Wed, Apr 27, 2011 at 2:30 PM, vasu punj <punjv@yahoo.com> wrote:
Though Tophat calls in Bowtie but they are different mapping tools. Details can be found in mannual of Tophat. For RNA-seq one may be stick with Tophat.
Vasu
--- On *Wed, 4/27/11, Austin Paul <austinpa@usc.edu>* wrote:
From: Austin Paul <austinpa@usc.edu> Subject: [galaxy-user] mapping with tophat vs. bwa To: galaxy-user@lists.bx.psu.edu Date: Wednesday, April 27, 2011, 4:20 PM
Hello,
I am getting what seems to me to be strange results using two different mapping tools in Galaxy. I am mapping illumina RNA-seq data and with tophat, while setting # alignments to 1, I get around 15-20% reads mapping. And when I use bwa, I am getting around 75% reads mapping. My reference is a collection of ESTs so the strength of tophat being a spliced read mapper is probably not being utilized, but I am surprised by the difference in
I for one am surprised and wish for others to chip in their 2 cents. Have u tried using bowtie instead of tophat? Since u are using est for ref. I am curious if bowtie will differ from top hat in this case. But afaik, one diff betw bowtie and bwa is that bwa allows for indels whilst bowtie doesn't. it might be useful if you can provide more info on the different parameters u used for both ur analysis, Cheers Kevin On 28 Apr 2011 05:40, "Austin Paul" <austinpa@usc.edu> wrote: the
number of reads mapping between the two. Any thoughts?
Austin
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participants (3)
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Austin Paul -
Kevin Lam -
vasu punj