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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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how to use a TE library from different accession as input to extract TEs? #9

Closed bioteksampath closed 6 years ago

bioteksampath commented 6 years ago

Hi I found this tool is really interesting and I like to use it for my research. I have a TE library generated from canola_A genotype in fasta and gff format and I like to use the same library to retrieve TE from Canola_B (different genotype) accession. how can I this canola_A TElibrary as input to extract the **all the TE members** ( expecting more copies in Canola_B) from Canola_B.

I believe that your suggestions will be really helpful.

Thanks & regards sam

oushujun commented 6 years ago

Hi Sam,

Thank you for using our method! If you think the canola A has a better genome quality and the two genome has no difference in LTR family despite different copy number, you can use the library on canola B. Otherwise it's more recommended to scan LTR again on the B genome, and combine both fasta libraries together for more a comprehensive annotation. You may use RepeatMasker for whole-genome annotation with your custom library.

Let me know if you have more questions. Thanks!

Best, Shujun

On Jan 18, 2018 11:52 AM, "bioteksampath" notifications@github.com wrote:

Hi I found this tool is really interesting and I like to use it for my research. I have a TE library generated from canola_A genotype in fasta and gff format and I like to use the same library to retrieve TE from Canola_B (different genotype) accession. how can I this canola_A TElibrary as input to extract the all the TE members ( expecting more copies in Canola_B) from Canola_B.

I believe that your suggestions will be really helpful.

Thanks & regards sam

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bioteksampath commented 6 years ago

Hi Shujun, Thanks for your prompt reply. Yes, I can use Repeatmasker to quantify the repeat proportion. But my aim is to retrieve the members of each family in redundant to see the difference between both genotypes.

so, how can I use LTRreteriver to extract members directly from fasta sequences AS INPUT but not with screen outputs of LTRfinder, LTRharvest or MGEScan.

Thanks sam

oushujun commented 6 years ago

Hi Sam,

If I understand correctly, you want to extract sequences of all intact LTR elements and compare them between genomes. It's possible, but not directly, and may involve in some coding.

First you can use the pass.list file to get the coordinates of all intact elements, then use the script bin/call_seq_by_list.pl to retrieve these sequences from genome. Usage see -h or the manual. Then using the intact sequence, you can do BLAST to locate intact elements in genome B. You may need some filtering to get full length elements from the BLAST result.

Hope these help!

Best, Shujun

On Jan 18, 2018 3:20 PM, "bioteksampath" notifications@github.com wrote:

Hi Shujun, Thanks for your prompt reply. Yes, I can use Repeatmasker to quantify the repeat proportion. But my aim is to retrieve the members of each family in redundant to see the difference between both genotypes.

so, how can I use LTRreteriver to extract members directly from fasta sequences AS INPUT but not with screen outputs of LTRfinder, LTRharvest or MGEScan.

Thanks sam

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bioteksampath commented 6 years ago

Thanks again Shujun, I will try and get back to u if necessary!

oushujun commented 6 years ago

Good luck!

On Jan 18, 2018 3:52 PM, "Sam" notifications@github.com wrote:

Thanks again Shujun, I will try and get back to u if necessary!

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