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Mapping Reads to Reference Genome (Statistics)

Hello,

I try to know the rate of mapping, overall error rate... of my sequences so I wanted to know a good mapping tool that gives me general statistics of mapping of my sequences.

Do you have any suggestions?

Thank you

mapping mapping tools error rate alignment ngs
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updated by EVR EVR • written by midox midox

Please specify which data you have (RNA-seq, DNA-seq, Illumina, Ion torrent, PacBio)...

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written by WouterDeCoster WouterDeCoster

PacBio and Nanopore Reads.

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written by midox midox

BWA for long reads I think is the best option.

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written by Buffo Buffo

Exactly, e.g. bwa mem -x ont2d.
GraphMap is also a good alternative, but slow.

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written by WouterDeCoster WouterDeCoster

1 answer

Try tophat2 ,Stringtie and all most tools will give you a summary of how many reads of total mapped onto genome.

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written by EVR EVR

I tried with Blasr but it gives me a rate file of the mapping of each sequence that's why I want a tool that gives me general statistics of all sequences file. I will try them thank you.

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written by midox midox

i want for DNA but tophat2 and Stringtie are for RNA!

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written by midox midox

And how should EVR know that if you don't tell us?

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written by WouterDeCoster WouterDeCoster

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