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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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align #19

Closed afadda91 closed 5 years ago

afadda91 commented 6 years ago

hi, in the discovery phase, i don't really get the difference between using the align option or not. I tried both with no difference. Can you explain please?

thanks,

tk2 commented 5 years ago

Apologies for the delay. If you provide fasta files of TE sequences (via -eref), then the discordantly mapped reads will be aligned to these sequences to assign the putative TE type.