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Old 10-05-2010, 05:10 PM   #1
seq7
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Default More Unique ELAND Alignments Than Reads?

Can anyone explain to me why I am finding more unique alignments in my eland_results file than I have reads in my sequence file?

wc -l s7_sequence.txt
5808194 (23232776 / 4)
grep -c " U[0,1,2] " s7_eland_result.txt
6371019

It doesn't make sense to me that the uniquely aligned sequence count should be greater than the total sequences read...

Thanks for your advice!
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Old 10-05-2010, 09:45 PM   #2
dawe
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Default

Quote:
Originally Posted by seq7 View Post
Can anyone explain to me why I am finding more unique alignments in my eland_results file than I have reads in my sequence file?

wc -l s7_sequence.txt
5808194 (23232776 / 4)
grep -c " U[0,1,2] " s7_eland_result.txt
6371019

It doesn't make sense to me that the uniquely aligned sequence count should be greater than the total sequences read...

Thanks for your advice!
I believe your grep is counting twice some stuff. First of all you shouldn't include a comma in square brackets, they define the alternative characters. And what does

Code:
wc -l s7_eland_result.txt
output?
Anyway, the correct grep for you is:

Code:
grep -cw U[012] s7_eland_result.txt
In the end, the s_7_sequence contains the filtered and uniquely mapped reads, doesn't it? (I may be wrong, it's a long time since I've used illumina output)

d
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Old 10-06-2010, 08:16 AM   #3
seq7
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wc -l s7_eland_result.txt
9196920

grep -cw U[012] s7_eland_result.txt
6371019

sequence.txt is filtered output.
eland_result.txt is unfiltered ELAND alignment output.

Thanks for the reply!
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