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tk2 / RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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Is RetroSeq still able to handle split reads? #14

Closed pyrevo closed 5 years ago

pyrevo commented 7 years ago

Dear @tk2,

I'm starting to use RetroSeq v1.5. From my understanding, the program is able to search for split reads using the -srmode parameter. However when I print out the help page from the discover function of RetroSeq 1.5, I obtain a different set of parameters with respect to the tutorial page of the Wiki.

Thus, I'm wondering if this version of RetroSeq is still able to handle split reads.

Thanks, Massimiliano.

tk2 commented 5 years ago

Hi - yes it will now use split reads by default, no need to specify it on the command line.