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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