Thread: subread
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Old 06-05-2013, 02:19 AM   #10
shi
Wei Shi
 
Location: Australia

Join Date: Feb 2010
Posts: 235
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Dear Jon and sdriscoll,

sdriscoll' explanation is correct.

Both subread and subjunc need users to specify the minimum and maximum insert lengths. The parameters --mindist and --maxdist are provided for this purpose. The minimum and maximum insert length can be calculated as mindist + length of read2 + 1 and maxdist + length of read2 + 1, respectively. However I think I do agree that these two parameters seem confusing. Probably it is better to specify the minimum and maximum insert lengths directly. We will change them in the next release.

We do not like redefining things unless absolutely necessary. We do not use the the -inner-mate-distance because we do not consider this in our read mapping.

Many thanks for your helpful comments.

Best wishes,

Wei
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