# This folder contains output files related to transposable elements in the golden eagle. ############################ ##### RepeatProteinMask #### ############################ ## version: 4.0.2 ## command: RepeatProteinMask -noLowSimple -pvalue 1e-4 -engine abblast kmer70-v2-min200-scaffolds.fa ## output files: ge_v2_all.annot ############################ ###### RepeatMasker ######## ############################ ## RepeatMasker version 4.0.2 ## RepeatMaskerLibrary-20130422 version ## command: RepeatMasker -nolow -no_is -norna -dir . \ -lib RepeatMaskerLib.embl.lib \ kmer70-v2-min200-scaffolds.fa ## output files: repeatmasker_kmer70-v2-min200-scaffolds.fa.masked repeatmasker_kmer70-v2-min200-scaffolds.fa.tbl ############################ ####### RepeatModeler ###### ############################ ## version: 1.0.7 ## command: BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.fa RepeatModeler -database goldenEagle_v2_tmp RepeatMasker -nolow -no_is -norna -dir . -lib Ach-v2.consensi.fa.classified kmer70-v2-min200-scaffolds.fa ## output files: Ach-v2.consensi.fa.classified repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked repeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl ############################ ########### trf ############ ############################ ## version: 4.04 ## command: trf kmer70-v2-min200-scaffolds.fa 2 7 7 80 10 50 200 -f -h ## output files: kmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200.dat ############################ ############################ ##### To summarize... ###### ############################ # To get the size of each file. Except for the readme txt file (I am still # editing it), others should have the same sizes. ## command: ls -lt * # output: -rw-r--r-- 1 ji20 fors 1641 Apr 18 15:17 GoldenEagle_TE_readme.txt -rw-r--r-- 1 ji20 fors 90698 Apr 17 14:31 Ach-v2.consensi.fa.classified -rw-r--r-- 1 ji20 fors 1581090178 Apr 17 14:24 repeatmasker_kmer70-v2-min200-scaffolds.fa.masked -rw-r--r-- 1 ji20 fors 2054 Apr 17 14:23 repeatmasker_kmer70-v2-min200-scaffolds.fa.tbl -rw-r--r-- 1 ji20 fors 78808626 Apr 17 14:22 RepeatMaskerLib.embl.lib -rw-r--r-- 1 ji20 fors 15733890 Apr 17 14:21 ge_v2_all.annot -rw-r--r-- 1 ji20 fors 1581090178 Jan 4 12:36 repeatmodeler_kmer70-v2-min200-scaffolds.fa.masked -rw-r--r-- 1 ji20 fors 2059 Jan 4 12:36 repeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl