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Old 08-02-2017, 10:00 AM   #1
daddyodevil
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Default How to use mirna and mrna sequences in bowtie2?

I have two files.

1. An mrna file in which each line looks like -

NR_030382 chr1:100154611-100178513 tattaggttggtgcaaaagtaattgtggtttttgcctgtaaaag

2. An mrna file whose lines are like -

>hsa-miR-576-3p MIMAT0004796
AAGAUGUGGAAAAAUUGGAAUC

Now if i am not wrong, the thing should be like this
> mrna is from 3'utr, so i need to reverse it since mirna is also from 3'
> now considering i am doing 6mer, i need to skip the first character from each sequence from mirna, then search the mrna file for the existence of its compliment

How do I achieve this using bowtie2 ?

Please consider the fact that I am just a regular computer programmer and this is my first time encountering anything related to bioinformatics. I think i'll be needing to do this for 7mer, 8mer and 7mer+a1 also.


P.S - This was of no help, http://seqanswers.com/forums/showthread.php?t=72252
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