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In tandem repeats, it's often important to know whether reads fully span a tandem repeat in order to know whether the ALT or REF call is actually correct. I'd expect it would be useful to have an an…
jzook updated
7 years ago
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Here is an example:
![360截图170810316377110](https://user-images.githubusercontent.com/22489982/170950160-485009d1-61d4-43f5-a8d7-3145a56022b8.png)
The coverage depths of A, B, B' and C are even, s…
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Hi,
I noticed you currently use version 4.3 of the VCF specification for tandem repeats. However, version 4.3 does not provide guidelines on handling tandem repeats, whereas version 4.4 does. Do y…
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Hi,
Thank you for developing the excellent `TRGT` tool. I've read your paper "_Resolving the unsolved: Comprehensive assessment of tandem repeats at scale_". To gain a better understanding, I've als…
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Hello,
I have a hybrid plant genome with two haplotypes (Hap#1=1.6Gb with 22 chromosomes and Hap#2=1.8Gb with 24 chromosomes). I wanted to mask the genome, but RepeatMasker seems to be stalling in…
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Hi @oushujun,
Within the Dasheng LTR, there exists a tandem repeat, but according to the current filtering strategy of LTR_retriever, it seems to be filtered out. Below is a Dasheng LTR scn record …
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I am failing to detect a long tandem expansion expansion in STR region.
All other tandem repeat expansions are detected as expected but they are much shorter and covered by at least some spanning…
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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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I used Kraken2+Bracken to quantify the composition of microbes in my metagenomic data with pre-build database (PlusPF). However, I found there are more than 1000+ reads were assigned to species A. Aft…