Mapping Reads to Reference Genome (Statistics)

Question

[midox]

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

[WouterDeCoster]

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

[midox]

PacBio and Nanopore Reads.

[Buffo]

BWA for long reads I think is the best option.

[WouterDeCoster]

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

Answer 1

[EVR]

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

[midox]

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.

[midox]

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

[WouterDeCoster]

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