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-   -   tmap mapall usage (http://seqanswers.com/forums/showthread.php?t=31040)

guil 06-12-2013 05:51 AM

tmap mapall usage
 
Hello everybody,

I camming from "bowtie world" and illumina sequencing...

but now I'm received a ion proton library and I want mapp that reads in a reference genome... I've found that TMAP tool is a better tool than bowtie and soap for ion proton reads...

I've no success in using the mapall algorithm

when I trying a error happens in "tmap_map_opt_check"

probably, there are some options that weren't used... but which one??
the manual didn't show any usefull information about that...

does anybody have a template for tmap mapall default commands?

like:
tmap mapall -f reference.fas -r lib.fastq -s out.sam etc.....


thanks

nilshomer 06-29-2013 08:07 PM

Quote:

Originally Posted by guil (Post 107439)
Hello everybody,

I camming from "bowtie world" and illumina sequencing...

but now I'm received a ion proton library and I want mapp that reads in a reference genome... I've found that TMAP tool is a better tool than bowtie and soap for ion proton reads...

I've no success in using the mapall algorithm

when I trying a error happens in "tmap_map_opt_check"

probably, there are some options that weren't used... but which one??
the manual didn't show any usefull information about that...

does anybody have a template for tmap mapall default commands?

like:
tmap mapall -f reference.fas -r lib.fastq -s out.sam etc.....


thanks

The mapall command requires you to specify the mapping algorithms, so something like:
tmap mapall -f reference.fas -r lib.fastq -s out.sam map1 map2 map3

See: https://github.com/iontorrent/TMAP/b.../tmap-book.pdf


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