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I want to know if I should remove the rows indicated with asterisk from my further analyses?
I have masked the contigs assembly of a drosophila species on the custom made library and I have too man…
xyz0o updated
2 years ago
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Hi Shujun,
When we run EDTA,we met an error,
"No such file or directory at /public1/home/sc61338/01_software/anaconda3/envs/EDTA/share/EDTA/util/TE_purifier.pl line 103.
Input file "Solanum…
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When running RepeatMasker on genome sequenced assembled from HiFi long reads, significant repetitive portions of scaffolds are left unmasked (sometimes up to 10% of total bases). This has a negative i…
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Hello,
I have run sedef on the zebrafish reference without issues in the past, but I tried running it using a recently published version of its chromosome 4 (reference: https://www.nature.com/artic…
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First of all, thank you for the wonderful tool! I just have a newbie question regarding best practices with regard on genome masking.
I am working on fungi annotation and I am using `EDTA` + `Repea…
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Hi there,
We are using CIRI-long in some data we've generated. We've read through the article and found that the algorithm deals with the possibility that naturally occurring tandem repeats are con…
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Hello,
I am trying to understand dnaPipeTE outputs. Specifically I am trying to figure out how are the numbers in Counts.txt calculated. When I look into reads_per_component_and_annotation file and…
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Hello.
I tried to run 'RepeatMasker -s -gff -lib pn-families.fa -xsmall -pa 64 pn.genome.fasta' and got an error.
I thought it was a memory problem. So I split my genome file.
When running 'RepeatM…
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Hello,
I am rerunning the last push in the same folder and get errors, here is the STDOUT and STDERR
This is a follow-up of this issue:
https://github.com/oushujun/EDTA/issues/10
```
./EDTA/ED…
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I'm trying to perform the steps listed under "AmpliCoNE usage with other reference genomes / species". Under step 1, one of the files needed is BED format output from RepeatMasker.
I'm having some …