Hello everyone,
I am working with paired-end SOLiD data, and I am not sure how to handle it.
1) What exactly is the difference between the F3 and F5 reads? Is the F5 reversed?
2) I'm using BWA for the analysis. How do I use it with paired-end? In the documentation it says 'file 1' and 'file 2', but I don't know which is which.
I have tried to run it both ways and in both times I got very few variants - 3000, 5000 while expecting 50000.
I have a color-space reference index, and I used the -c parameter in the alignment. Am I missing something?
3) Does the csfasta conversion work differently with paired-end data?
Thanks a lot,
Amit
=]
I am working with paired-end SOLiD data, and I am not sure how to handle it.
1) What exactly is the difference between the F3 and F5 reads? Is the F5 reversed?
2) I'm using BWA for the analysis. How do I use it with paired-end? In the documentation it says 'file 1' and 'file 2', but I don't know which is which.
I have tried to run it both ways and in both times I got very few variants - 3000, 5000 while expecting 50000.
I have a color-space reference index, and I used the -c parameter in the alignment. Am I missing something?
3) Does the csfasta conversion work differently with paired-end data?
Thanks a lot,
Amit
=]
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