Discrepancy Between Expected and Actual Results in solo_intact_ratio.pl #189
Description
Dear Shujun,
I'm sorry to disturb you during your busy schedule, but now I have a question that I have to ask you.
I ran the following code:
perl find_LTR.pl -lib CM334.fa.LTRlib.redundant.fa > lib.LTR.info
perl solo_finder.pl -i CM334.fa.out -info lib.LTR.info > solo_list
perl intact_finder_coarse.pl CM334.fa.out > intact_list
perl solo_intact_ratio.pl solo_list intact_list > solo_intact_ratio
The result I got from solo_intact_ratio is as follows:
LTR_fam Solo_count Intact_count Solo-Intact-ratio
Chr01:100492535..100492783_LTR 17 2 8.5
Chr01:100617036..100618237_LTR 43 4 10.8
Chr01:102776141..102776529_LTR 9 0 inf
Chr01:103886370..103887460_LTR 288 20 14.4
Chr01:1061961..1062919_LTR 52 33 1.6
Chr01:107650169..107652224_LTR 706 305 2.3
Chr01:107669114..107670605_LTR 65 7 9.3
Why do the values in the LTR_fam column look so strange? Could there be an issue with my file processing or did I choose the wrong input files?
Below is the information of my input files. I would appreciate your advice and help.
head intact_list
Chr09:257681437..257681603_LTR
Chr05:117720066..117722833_LTR
Chr01:65331735..65331897_LTR
Chr12:222483934..222484192_LTR
Chr03:254622779..254623095_LTR
Chr03:55146..57693_LTR
Chr09:265061262..265062177_LTR
Chr03:21455926..21456395_LTR
Chr11:221750659..221751721_LTR
Chr01:1061961..1062919_LTR
head solo_list
Chr01 44839 46925 Chr01:44839..46925 Chr09:8838064..8840329_LTR 0.920564872021183
Chr01 59717 60487 Chr01:59717..60487 Chr03:266772255..266773021_LTR 1.00391134289439
Chr01 102621 105009 Chr01:102621..105009 Chr09:8838064..8840329_LTR 1.05383936451898
Chr01 168404 169021 Chr01:168404..169021 Chr05:226683519..226684164_LTR 0.955108359133127
Chr01 208636 209566 Chr01:208636..209566 Chr04:236886772..236887721_LTR 0.978947368421053
Chr01 214785 214902 Chr01:214785..214902 Chr06:201259605..201259730_LTR 0.928571428571429
Chr01 255066 255185 Chr01:255066..255185 Chr06:201259605..201259730_LTR 0.944444444444444
Chr01 271657 272060 Chr01:271657..272060 Chr09:5709599..5710001_LTR 1
Chr01 280831 281242 Chr01:280831..281242 Chr09:5709599..5710001_LTR 1.01985111662531
Chr01 285832 285950 Chr01:285832..285950 Chr06:201259605..201259730_LTR 0.936507936507937
head lib.LTR.info
Chr01:365766..365919_LTR#LTR/Copia 1 154 154
Chr01:370461..370614_LTR#LTR/Copia 1 154 154
Chr01:857273..859807_LTR#LTR/Gypsy 1 2535 2535
Chr01:864970..867541_LTR#LTR/Gypsy 1 2572 2572
Chr01:1061961..1062919_LTR#LTR/Gypsy 1 959 959
Chr01:1067418..1068387_LTR#LTR/Gypsy 1 970 970
Chr01:1256931..1257336_LTR#LTR/Copia 1 406 406
Chr01:1261967..1262362_LTR#LTR/Copia 1 396 396
Chr01:1394902..1395670_LTR#LTR/unknown 1 769 769
Chr01:1397677..1398446_LTR#LTR/unknown 1 770 770