updated README
now will compare RelocaTE output, not characaTErizer output
will now use RelocaTE blat, no need to run again
trying to find non-LTR, some changes, but so far not sucessful
compares characaTErizer output -- used to be called compare_strains.pl
change TSD=NONE to UNK
Updated README
fixed path
fixed path
rm shellscript in do-it-now mode
typos
typo
fixed BWA link
add count of seqs that match to uniq regions
added option for nonLTR elem, (blat -noTrimA)
changed location of existingTE.blatout
if results dir exists, delete it
will convert fq2fa even if only 1 needs to be converted
corrected file count for convert fq2fa
updated README for v1-0-4