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Making TE.gtf using Genome.fa.out file made by RepeatMasker? #83
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Hi, Thanks for your interest in the software.
There are a couple of things you might need to consider/change in your file before running the script:
If you make changes 1 to 3 as listed above, then I might try running the script with the following parameters: perl makeTEGTF.pl -c 5 -s 6 -e 7 -o 9 -t 10 -f 11 -S 1 [your altered output] > [TE GTF] I've attached a version of your file that should work with the above command line. Note that the script will remove most simple repetitive sequences and short non-coding RNA (e.g. tRNA) Thanks. |
Well, I modified your I correct your codes, firstly using multi-space rather than tab as splitter, than
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Sounds good. Let us know if you encounter any issues. Thanks. |
Hi @olivertam ! I'm trying to run the makeTEgtf.pl script but I keep getting this error message on every line:
Any idea why it doesn't work? Thanks a lot! |
Hi, Thank you for your interest in the software.
Thanks. |
Hi, I used this command line: I used the command provided and the output looks like this:
\\ |
Glad to hear that the error has been resolved. All the best. |
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days |
I called TE elements using RepeatModeler and RepeatMasker from genome of Phaeodactylum tricornutum and here is the
out
file by RepeatMasker:Phaeodactylum_tricornutum.ASM15095v2.dna_sm.toplevel.fa.out.gz
Can we make TE.gtf file using such
out
files? Are there any demo?The text was updated successfully, but these errors were encountered: