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My calls for chrX are all in the region between PAR1 and PAR2, so they are not in the pseudoautosomal region.
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Thanks @d-cameron, yes, multiple alignments for R1 and R2 of the same template have the same name, and I only know how to distinguish if t…
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The [SAM file format specifications][1] states:
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> I'm absolutely new in these waters so I'd very much appreciate some help.
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