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This is the same issue reported in #82 , we ran RepeatModeler2 on a 1.1gb genome four times but still get the same issue. We also ran it using the docker image but still catch the same error.
The s…
niccw updated
3 years ago
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Hello, here's my issue:
I ran tandem-genotypes on long reads (Oxford Nanopore) on a RepeatMasker locus and obtained this result:
`
chr11 70487135 70487173 TGC SHANK2 coding 0,0,0,0,0,0,0,0,0,0,…
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Hi, I'm using `tandem-genotypes` to find tandem repeats(TR) from our human PacBio HiFi reads. I found a real TR which is not successfully called by `tandem-genotypes`. I used a repeat-masking genome t…
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Hi,
I would like to ask about ABRA realignment of single-fragment (non-paired) reads around regions where there is a poly-A or poly-T or low complexity region where bowtie2/bwamem are unable to prope…
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Dear developers,
Following a brief discussion on Twitter, I will here present some stats from comparing **Bonito 0.3.2** against **Guppy 4.2.2** (HAC and Fast) basecalls using an Nvidia RTX 3090 on…
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**sequence_alteration** needs a term or terms to refer to STR alleles ('microsatellites') that differ in repeat unit number from the reference. Existing terms under _sequence_alteration_\* are not app…
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Hi, I have four more questions.
1. You defined five types inovirus in the result files: prophage, complete, integrase, DR, tRNA. But the type, complete, seems have no att sites. Are the complete …
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I am trying to build a lobSTR model for the non-PCR-free nano model. I have a BAM file generated by BWA-MEM. The program crashes as follows.
```
_______
\\ // / …
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## Problem description
While using LTRharvest this error pops up：
```
Assertion failed: (refrng.start leftLTR_5), function gt_removeoverlapswithlowersimilarity, file src/ltr/ltrharvest_stream.c, …
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I hope this message finds you well. I am currently exploring smoothxg algorithm. I came across a statement in the paper that raised some questions for me:
"A key issue is that pairwise alignments d…