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Hello, @kirilenkobm and @MichaelHiller,
Thanks for creating this tool - I was looking for an option to run `lastz` genome-to-genome alignment on multiple threads and ended up here.
I was submitt…
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Hi,
I am running BRAKER v2.1.6 on a ~3Gbp soft-masked shark genome (~2000 contigs) and am running the BRAKER pipeline with RNA-Seq data. The run finishes without any problems according to the `bra…
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Hello,
I was getting this error message when running the pipeline: `Traceback (most recent call last):
File "/rds/user/hpc-work/SoloTE_1.08/SoloTE_pipeline.py", line 321, in
marketmatrix_lin…
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I'm getting an error message `Got an unexpected character paf cigar string: i` at the `paf_to_bed` stage. Any help for solving this would be much appreciated.
I am aligning 7 plant genomes (each ar…
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The tool [RepeatMasker ](https://usegalaxy.no/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.1) has a parallel option which is set as:
`-parallel \${GALAXY…
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I'm trying out the new SV RepeatMasker annotation feature in GRIPSS 2.2 but an error is raised during parsing of the RM
repeat library file.
This seems to be caused by two entries in the file that…
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Hello,
Thank you very much for developing and managing this strong software!
I have a question about the output file of RepeatMasker. I really want to know what is the meaning of the milliDiv (= B…
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Hello Robert,
I am using RepeatMasker version 4.1.1 installed in Linux via conda.
I constructed a library using known Arabidopsis TEs with their classification following RepeatMasker's naming sc…
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Dear ExplorATE developer,
I've run ExplorATE shell script on my data. Everything is fine but I am not able to retrieve usable transposon IDs.
I've run this
bash ${EXPLORATE} mo -p 12 \
-b /u…
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Hi,
I just masked my genome assembly and then used the script rmOutToGFF3.pl to convert the out file to gff3. The problem is that, whatever downstream software I use with this gff, the file is not …