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Old 05-11-2021, 01:03 PM   #681
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Location: United States

Join Date: May 2021
Posts: 1
Default Is mapping stochastic?

Hey, did a little test run mapping sequences against a reference fasta that contains two identical sequences called >one and >two, then repeated the process with the sequences renamed to >three and >four. The amount of reads mapping to each were as follows:

1st run:

>one: 47,699
>two: 330

2nd run:

>three: 47,688
>four: 338

BBmap options were all default, just minidentity = 90 and T=12

How come that (1) BBmap apparently misses some reads that map on the first sequence and then maps them on the second, identical sequence, and (2) how come the runs give different results?

Just curious, my apologies if this was addressed elsewhere!

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