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I am interested in identifying repeat sequences that are unique to single chromosome centromeres. Could you clarify if your code is capable of detecting such unique repeat sequences within centromeric…
frvcw updated
1 month ago
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Hi, we want to use ```tandem-genotypes``` to detect tandem repeats in genome-wide data. Following your instructions, I must first align my sequence using last before running ```tandem-genotypes```. U…
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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…
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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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Implement a WDL task and evaluate the use of the noise-cancelling repeat finder (NCRF). From the manuscript (https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz484/…
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Hi Gao,
I tried to retrieve the repeated subunits from the long read and feed it into other consensus calling methods (such as Medaka by ONT or majority voting).
According to the README:
subPos:…
zztin updated
4 years ago
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Hello!
To detect ASD-related tandem repeat loci in my data, I'm refering to Trost et al. (2020). While I run an outlier analysis in EHdn, I have some questions.
1. I knew that depth-normalized c…
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Hi,
I would like to use this model in a plant genome and WGS data. The Variant catalog file is a required input, I think there is a hypothetical strategy to achieve this goal,
step1: identify th…
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Hi!
I have a patient sample with a known gene fusion/genomic translocation (i.e. PAX5::ETV6).
Sniffle 2.0.7 did call this BND in the vcf by running `sniffles --input mysample.bam --vcf out.vcf --n…
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Basically I have a somewhat plausible long read assembly with several tandem repeats. When feeding it to Unicycler w/ `--existing_long_read_assembly` together w/ Illumina short reads, the assembly get…