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bcgsc / NanoSim

Nanopore sequence read simulator
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Regarding simulate output #122

Closed aman21392 closed 3 years ago

aman21392 commented 3 years ago

So I ran nanosim through transcript mode. So I get 2 fasta file, one is control_simulate_aligned_reads.fasta control_simulate_unaligned_reads.fasta

So I just want to know that the unaligned_reads.fasta are also simulated or they are as it is without simulated reads. Please just clarify it. Thanks in advance

cheny19 commented 3 years ago

They are simulated reads with high error rates, so theoretically they cannot be aligned to the reference.

aman21392 commented 3 years ago

So it means we can not use those reads further for any analysis. Thanks

SaberHQ commented 3 years ago

Whether to use or not to use "unaligned" read set depends on your analysis and research problem. In general, one would only use the "aligned" read set in any downstream analysis.

I also suggest you to take a look at Trans-NanoSim paper in which you can get more info about unaligned read sets. Let us know if you have any question. Thanks.

https://academic.oup.com/gigascience/article/9/6/giaa061/5855462

aman21392 commented 3 years ago

ok thanks, I look at this paper.