[galaxy-user] Help!! Tophat paired end reads

[杨继文]

Hi,
I am very confused by my mapping. Please help me figure out what's wrong with 
my operation.
 
I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to map 
these reads.
After mapping, I used IGV to have a look at the mapping.
 
I can see that some of the reads fall into exons or span exons (splice 
junction). These reads seem to fit very well. However, I can also see a lot 
reads mapped to non-coding region. Are these reads from pre-mRNA? or my mapping 
was wrong? Did anybody have similar experience??  
 
Furthermore, I can see huge enrichment of reads in 3' UTR (much much more than 
the coding region).  Is this normal?  Is this caused by the rRNA depletion 
method ?
 
Looking forward to your reply
Jiwen ___
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Re: [galaxy-user] Help!! Tophat paired end reads

[Jennifer Jackson]

Hi Jiwen,

The bioinformatics part of your analysis sounds as if it went fine, so 
that is good news. This list may not be the best place to get feedback 
about library construction methods, but we can see who has help to offer.


I did a quick search myself and found this recent publication that 
includes a comparison of rRNA depletion methods with mapping profiles:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027288

Best,

Jen
Galaxy team

On 4/15/12 8:24 AM, 杨继文 wrote:

Hi,
I am very confused by my mapping. Please help me figure out what's wrong
with my operation.
I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to
map these reads.
After mapping, I used IGV to have a look at the mapping.
I can see that some of the reads fall into exons or span exons (splice
junction). These reads seem to fit very well. However, I can also see a
lot reads mapped to non-coding region. Are these reads from pre-mRNA? or
my mapping was wrong? Did anybody have similar experience??
Furthermore, I can see huge enrichment of reads in 3' UTR (much much
more than the coding region). Is this normal? Is this caused by the rRNA
depletion method ?
Looking forward to your reply
Jiwen




___
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Galaxy analysis and other features on the public server
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use the Galaxy Development list:

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--
Jennifer Jackson
http://galaxyproject.org
___
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,
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