Hi everyone!
I am a bioinformatics student and I have just started dealing with SOLiD reads.
The sequenced reads I have are full of dots ("."). This is an example:
>1_459_10_F3
T1.0212.2323.2320321323213320323212213...20...20...
>1_480_41_F3
T1.1213.2223.1320112233101130002201222...11...03...
>1_482_41_F3
T1.0111.1023.2320110113122032121122101...21...13...
I have read that those dots are bases that could not be identified and, when translated, would be "N"s.
My question is how to deal with this reads? Discard the entire read? Trim the read? (I think trimming would generate very short reads that would not be good for alignment.)
Does anyone knows how the aligners (bowtie, novoalign, maq, soap, etc) deal with it?
Thanks in advance!
I am a bioinformatics student and I have just started dealing with SOLiD reads.
The sequenced reads I have are full of dots ("."). This is an example:
>1_459_10_F3
T1.0212.2323.2320321323213320323212213...20...20...
>1_480_41_F3
T1.1213.2223.1320112233101130002201222...11...03...
>1_482_41_F3
T1.0111.1023.2320110113122032121122101...21...13...
I have read that those dots are bases that could not be identified and, when translated, would be "N"s.
My question is how to deal with this reads? Discard the entire read? Trim the read? (I think trimming would generate very short reads that would not be good for alignment.)
Does anyone knows how the aligners (bowtie, novoalign, maq, soap, etc) deal with it?
Thanks in advance!
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