More Unique ELAND Alignments Than Reads?

seq7 · 10-05-2010, 05:10 PM

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 · 10-05-2010, 09:45 PM

Quote:

Originally Posted by 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!

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

seq7 · 10-06-2010, 08:16 AM

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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10-05-2010, 05:10 PM	#1
seq7 Junior Member Location: Chicago Join Date: Oct 2010 Posts: 2	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!

10-06-2010, 08:16 AM	#3
seq7 Junior Member Location: Chicago Join Date: Oct 2010 Posts: 2	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!