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Old 07-19-2011, 09:18 AM   #1
PFS
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Default Bowtie call to get unique, multi-hits and nonmatching reads

Hello there,

I want to estimate (1) the number of reads that map uniquely (in one place only), (2) the number of reads that map in multiple places and (3) the number of reads that do not map at all.

Is this the correct bowtie call?

-m 1 --un nomatch_reads.txt -- max multihits_reads.txt

Thanks!
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Old 07-19-2011, 12:56 PM   #2
kwatts59
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First find the number of reads that map at least once. To do this, run bowtie with "-k 1" option. Lets call this number K1.

Then run bowtie with the "-k 2" option. This will report up to two alignments per read. Lets call this number K2.

Subtracting the K1 from K2 gives the number of reads that mapped two or more times. Lets call this number K2p.

To find the number of reads that mapped exactly once, subtract K2p from K1.

To find the number of reads that did not map at all, just subtract K1 from the total number of reads in your sample.
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Old 07-19-2011, 01:05 PM   #3
chadn737
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Not sure if this is what you want, but a few months back I wrote a very simple perl script (probably not very good, I'm a biologist not a programmer, so my scripts tend to be brute force approaches) that will take a sam file and spit out the names of the reads that map more than once and how many times they mapped.

Now I can't even remember what I was using it for, but maybe it will help you get to where you need.
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Last edited by chadn737; 07-19-2011 at 01:21 PM.
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Old 07-07-2019, 07:18 AM   #4
brojee
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First locate the quantity of peruses that guide at any rate once. To do this, run necktie with "- k 1" alternative. Lets call this number K1.

At that point run necktie with the "- k 2" choice. This will report up to two arrangements for every read. Lets call this number K2.

Subtracting the K1 from K2 gives the quantity of peruses that mapped at least multiple times. Lets call this number K2p.

To locate the quantity of peruses that mapped precisely once, subtract K2p from K1.

To locate the quantity of peruses that did not outline all, simply subtract K1 from the complete number of peruses in your example.
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