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What to do if there are many unmatched reads after mapping?

What to do if there are many unmatched reads after mapping (WGS alignment)? Tried elongation and error reducing condensation in NextGene software and no help. What can be done to improve ref and input sequence match, in other words?

matching mapping alignment
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written by matveyspr • matveyspr

You need to give a bit more information about the technology used for the sequencing, the organism you are working on and the software you are using with specifications of parameters.

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written by WouterDeCoster WouterDeCoster

Illumina, M tuberculosis, NextGene software, default parameters, 2 elongation default cycles

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written by matveyspr • matveyspr

Take a sample of unmatched reads and blast at NCBI to make sure they are actually what you think they are. It is always safe to ensure that blast returns matches for the expected species.

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written by GenoMax GenoMax

Hello matveyspr!

We believe that this post does not fit the main topic of this site.

It is unclear what you are asking, what have you tried?

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Michael Dondrup Michael Dondrup

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