oushujun
commented
5 years ago Hi Shenglong,
You can use format 1 (-harvest_out) and give it to LTR_retriever with -inharvest. If you have more than one harvest out file for example, another output from LTRharvest, just aggregate them into one file and specify with -inharvest. Hope it helps!
Best, Shujun
On Sat, Jun 1, 2019, 8:43 PM slbai01 notifications@github.com wrote:
Dear Dr. Ou,
I want to use LTR_FINDER_parallel output file to calculate LAI by LTR_retriever.
Your modifications make it very fast compared to the previous single-threaded version. But the format of the output is not the same as before. How do I set parameters or use other scripts to convert to the previous format?
- old format (maybe I need this foramt)
Program : LTR_FINDER Version : 1.07
Predict protein Domains 4.669 second
Sequence: Contig10_pilon Len:17381955 [1] Contig10_pilon Len:17381955 Location : 71911 - 85359 Len: 13449 Strand:+ Score : 6 [LTR region similarity:0.952] Status : 11111010000 5'-LTR : 71911 - 73491 Len: 1581 3'-LTR : 83775 - 85359 Len: 1585 5'-TG : TG , TG 3'-CA : CA , CA TSR : 71906 - 71910 , 85360 - 85364 [GTGAA] Sharpness: 0.5,0.486 Strand + : PPT : [13/15] 83744 - 83758
Details of exact match pairs: 83791-83876[86] (22) 83899-83935[37] (24) 83960-84012[53] (1) 84014-84033[20] (34) 84068-84097[30] (15) 84113-84145[33] 71927-72012[86] (22) 72035-72071[37] (25) 72097-72149[53] (1) 72151-72170[20] (35) 72206-72235[30] (16) 72252-72284[33]
Details of the LTR alignment(5'-end): |83775 CTCGAGGACGAGT-AGG----AATTAAGCTTGGGGATGCTGATACGTCTCCAACATATCTATAATTTATGAAGTATTCATG | | ||| ||| | | || ||| | || | | *|||||||||||||| |||||||||||||||||||||||||| CATG-GGATAAGTCATGTTATAAGTAATCATGTGAA---TGATACGTCTCCAACGTATCTATAATTTATGAAGTATTCATG *****---|71911 ...... ......
- new format1
$head -20 genome.fa.finder.combine.scn
LTR_FINDER_parallel -seq genome.fa -size 5000000 -time 1500 -try1 1 -harvest_out -threads 28 -cut /share/home/programs/LTR_FINDER_parallel/bin/cut.pl -finder /share/home/programs/LTR_FINDER_parallel/bin/LTR_FINDER.x86_64-1.0.7/ltr_finder
LTR_FINDER args=-w 2 -C -D 15000 -d 1000 -L 7000 -l 100 -p 20 -M 0.85
predictions are reported in the following way
s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR) l(rLTR) sim(LTRs) seq-nr chr
where:
s = starting position
e = ending position
l = length
ret = LTR-retrotransposon
lLTR = left LTR
rLTR = right LTR
sim = similarity
seq-nr = sequence order
60774 69360 8587 60774 62502 1729 67625 69360 1736 96.1 0 Chr1 88505 98181 9677 88505 89925 1421 96758 98181 1424 97.7 0 Chr1 ......
- new format2
$head -20 ../02.LTR_Finder_old/genome.fa.finder.combine.scn index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity [NA] Chr1 60774-69360 1729,1736 8587 CAAAG N-N 62504-62518 N-N N-N N-N N-N -6 0.514,0.529 0.961 [NA] Chr1 88505-98181 1421,1424 9677 ATGTT N-N 96726-96740 N-N N-N N-N N-N +6 0.486,0.514 0.977 ......
Shenglong
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Dear Dr. Ou,
I want to use LTR_FINDER_parallel output file to calculate LAI by LTR_retriever.
Your modifications make it very fast compared to the previous single-threaded version. But the format of the output is not the same as before. How do I set parameters or use other scripts to convert to the previous format?
Shenglong