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.
Many thanks for maintaining RetroSeq - great tool!
After some performance tests, I just realised that the default parameter settings in your retroseq.pl -call raw description are actually not in line with the values set (currently: -reads = 10 and -q = 20). Maybe you could quickly replace the source script's lines 199-201 accordingly?
`[-depth Max average depth of a region to be considered for calling. Default is $DEFAULT_MAX_DEPTH.]
[-reads It is the minimum number of reads required to make a call. Default is $DEFAULT_READS.]
[-q Minimum mapping quality for a read mate that anchors the insertion call. Default is $DEFAULT_ANCHORQ.]`
Hi @tk2,
Many thanks for maintaining RetroSeq - great tool!
After some performance tests, I just realised that the default parameter settings in your retroseq.pl -call raw description are actually not in line with the values set (currently: -reads = 10 and -q = 20). Maybe you could quickly replace the source script's lines 199-201 accordingly?
`[-depth Max average depth of a region to be considered for calling. Default is $DEFAULT_MAX_DEPTH.]
[-reads It is the minimum number of reads required to make a call. Default is $DEFAULT_READS.]
[-q Minimum mapping quality for a read mate that anchors the insertion call. Default is $DEFAULT_ANCHORQ.]`
Cheers, Max