Mapping Reads to Reference Genome (Statistics)
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4.6 years ago
midox ▴ 270

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 • 1.3k views
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Please specify which data you have (RNA-seq, DNA-seq, Illumina, Ion torrent, PacBio)...

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PacBio and Nanopore Reads.

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BWA for long reads I think is the best option.

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

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4.6 years ago
EVR ▴ 570

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

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

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