More Unique ELAND Alignments Than Reads?

[seq7]

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!

[dawe]

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

wc -l s7_eland_result.txt

output?
Anyway, the correct grep for you is:

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

[seq7]

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!