search

qjiangzhao / TEtrimmer

TEtrimmer: a novel tool to automate manual curation of transposable elements
GNU General Public License v3.0
62 stars 2 forks source link

Questions about the final result file #25

Closed Song-10-YF closed 5 months ago

Song-10-YF commented 5 months ago

Dear Dr. Zhao,

Thank you very much for developing the software for automatic correction of TE annotations. I am also applying this process to correct my TE annotations. Does this software still correct at the level of consensus sequences? I would like to know how to obtain the final TE annotation file.

Looking forward to your reply.

Yan-Feng Song

qjiangzhao commented 5 months ago

Dear Yan-Feng:

Thanks you are interested in TEtrimmer.

By default, TEtrimmer won't do the whole genome TE annotation. But You can add "--genome_anno" option to enable that.

Yours sincerely Jiangzhao

Song-10-YF commented 5 months ago

Thanks! I'll try！ For tasks that have already completed, can I add "-ca --genome_anno" to obtain annotation files?

qjiangzhao commented 5 months ago

Yes. You can!

Song-10-YF commented 5 months ago

I tried using this command to re-analyze tasks that had already ended. The task quickly showed as completed, but it did not output an annotation file.

qjiangzhao commented 5 months ago

oh! I will write this to my list and fix this for the next version.

Anyway, TEtrimmer used RepeatMasker for the whole genome TE annotation. You can use: ''' RepeatMasker <path to/genome_file> -lib <path to/TEtrimmer_consensus_merged.fasta> -pa -dir -s -gff -xm -a ''' for the TE annotation.

Song-10-YF commented 5 months ago

OK, thank you very much!

qjiangzhao commented 5 months ago

no worries!