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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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LTR superfamily summary and distribution output #37

Closed bioteksampath closed 5 years ago

bioteksampath commented 5 years ago

Hi,

My LTR-retriever run does give all the outputs except three of the following. I just wonder how to get these as well, do i need to specify in my run?

The output of LTR_retriever includes: LTR family summary (.out.fam.size.list) LTR superfamily summary (.out.superfam.size.list) LTR distribution on each chromosome (.out.LTR.distribution.txt)

cmd used: /LTR_retriever -genome Bnigra_ref2_genome.fasta -inharvest Bnigra_ref2_genome.harvest.nonTGCA.scn -infinder Bnigra_ref2_genome.LTRfinder.scn -blastclust -L .9 -b T -S 80 -threads 10

Thanks a lot! Sam

oushujun commented 5 years ago

Hi Sam,

The parameter format you provided to blastclust needed to be adjusted. You may try:

/LTR_retriever -genome Bnigra_ref2_genome.fasta -inharvest Bnigra_ref2_genome.harvest.nonTGCA.scn -infinder Bnigra_ref2_genome.LTRfinder.scn -blastclust -threads 10

or if you want to customize parameters for blastclust other than the default, you may do:

/LTR_retriever -genome Bnigra_ref2_genome.fasta -inharvest Bnigra_ref2_genome.harvest.nonTGCA.scn -infinder Bnigra_ref2_genome.LTRfinder.scn -blastclust [-L .9 -b T -S 80] -threads 10

If the program runs correctly, it should produce the three files you are looking for. Could you paste here the STDOUT infomation? There may be some errors preventing it from generating these files. If you think it runs correctly, you may run these scripts alone:

perl /LTR_retriever/bin/fam_coverage.pl $genome.LTRlib.fa $genome.out $genome_size > $genome.out.fam.size.list

perl /LTR_retriever/bin/fam_summary.pl $genome.out.fam.size.list $genome_size > $genome.out.superfam.size.list

perl /LTR_retriever/bin/LTR_sum.pl -genome $genome -all $genome.out > $genome.out.LTR.distribution.txt

Please let me know if you need further help.

Best, Shujun

oushujun commented 5 years ago

You may reopen this issue if your problem is not solved. Thanks! Shujun

bioteksampath commented 5 years ago

yes, it worked after updating to the new version! Thanks oushujun.