masks for SOLiD paired-ends reads 35+50nt
Hi there,
I've gone through the Bfast manual and I found a suggestion for masks assuming reads of at least 50nt in section 7.1.2. The problem is that my paired reads do not have the same length (SOLiDv4, paired-end libraries not mate-pair libraries, they have different orientation), one has 35nt in length and the other one has 50nt. Do I need to use different masks in order to index the reference for reads with 35nt or it's OK if I use those masks suggested in the manual for 50nt reads also for 35nt reads?
Thanks in advance.
Best regards,
S.
Originally posted by nilshomer
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I've gone through the Bfast manual and I found a suggestion for masks assuming reads of at least 50nt in section 7.1.2. The problem is that my paired reads do not have the same length (SOLiDv4, paired-end libraries not mate-pair libraries, they have different orientation), one has 35nt in length and the other one has 50nt. Do I need to use different masks in order to index the reference for reads with 35nt or it's OK if I use those masks suggested in the manual for 50nt reads also for 35nt reads?
Thanks in advance.
Best regards,
S.
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