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Old 10-27-2011, 08:38 AM   #1
yjx1217
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Location: Houston

Join Date: Oct 2011
Posts: 13
Question Using MAQ to simulate illumina pair-end reads

Hello there, I was trying to simulate illumina pair-end reads by using MAQ for my project but ran into a couple of questions>>

1) when using "maq simutrain" command, the input fastq file should be a file that contain both left and right hand reads or just 1-end reads will also be fine or should I feed maq with two separated reads files(left-hand reads and right-hand reads respectively)?

2) when I run the command of "maq simutrain out.simupars.dat COLXLER_1.fastq", the maq prompt this information>>
maq: simulate.c:55: fqc_collect: Assertion `fqc->l_min == fqc->l_max' failed.
Does anybody know why?

3) the 3rd question is about the -d option of maq simulate command. In MAQ's document, it is said that -d is the " mean of the outer distance of insert sizes". I am not sure about the meaning here. For example, for 300bp fragments with both ends sequenced by 100bp reads, what value should I put here? 100 or 300?

Thanks very much and have a great day!
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