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Old 09-30-2010, 05:38 PM   #1
jay2008
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Default how to decide the other arm in miRNA sequencing

Hi,

I am using your excellent software novoalign. my question is:

when I use command: novoalign -d hg36.ndx -f s_1_0000_sequence.txt -a -m -l 18 -h90 -r A,

I got report like:

@SRR001342.63 S AAAATAAACAAATAGGG IIIIIIIIIIIIIIIII U 0 21 154 >gi|116010291 18213481 F . . .

there are two possible precursor miRNAs

5'----AAAATAAACAAATAGGG -------------- XXXXXXXXXXXXXXXXXX---

5'---- XXXXXXXXXXXXXXXXXX---------------AAAATAAACAAATAGGG ----

how can I decide which one is for align score 154 from the output?

thanks

Jian
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Old 09-30-2010, 08:43 PM   #2
zee
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The aligner will give you the best location(s) for the short read but in terms of deciding which one is the 5' or 3' miRNA this is not an alignment tool's decision.

Working with pileups of all your reads mapped to the genome and looking at relative abundance of 5' and 3' read pileups will give you some indication of which is the mature small RNA.
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Old 09-30-2010, 09:48 PM   #3
jay2008
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thanks zee,

I did not want to know which one is 5'. I want to know the alignment score is from which part. i.e. forward or backward.

for example in my previous example,
the read is mapped to between xxxxxxxxxx and yyyyyyy.
XXXXXXXXXXXXX--------AAAATAAACAAATAGGG---------YYYYYYYYYYYY

the short sequence "AAAATAAACAAATAGGG" may complementary binding to XXXXXXXXX or YYYYYYYYYYYY. I want to know the aligment score 154 is from which one, xxxxxxxxxx or yyyyyyyyy.

thanks
jian
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Old 09-30-2010, 10:49 PM   #4
sparks
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Hi Jian,

The score is from lower of the two possibilities but your right we don't indicate which one it is. The original idea was just to help locate which alignment was the precursor but not the orientation of the precursor. I can easily add the second location using field normally used for mate pair location in paired end processing.

I'll add it to the next release.

Colin
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Old 10-26-2010, 10:46 PM   #5
sparks
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Novoalign V2.07.03 is now available on www.novocraft.com.

Changes include reporting the location of the hair pin alignment (i.e. the xxxxxxxx or yyyyyy as requested by jay2008)
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