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Hello,
I have encountered a weird issue when using minimap2 to do whole genome alignment. My data conatins a short assembly A (haplotype) and a long assembly B (diploid). When I used the assembly A a…
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Hello,
I'm using seq_io to do some sliding window analysis of a 4Mb genome, but the size of the sequence remains limited. How should I configure my Rust program for the seqeunce size to be about 4M…
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I am currently conducting Whole Genome Bisulfite Sequencing (WGBS) data analysis using Bismark and plan to utilize a soft-masked genome, where all repetitive and low-complexity regions are marked with…
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I was wondering if there was any upper limit (either computationally or experimentally) in terms of the size of the genome(s) to run olivar on. I'm trying to design a primer set for multiple organisms…
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Hi Winnowmap Team,
I am trying to use winnowmap to do whole-genome alignments. In some cases, winnowmap is resulting in large unaligned regions like below:
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I am working on an HPC cluster with PBS PRO and not SLURM is there any way to execute the…
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Hello, I am trying to extract COI genes from raw Illumina sequences of cestodes to try and ID the hosts. I am using the cestodes as a proof of concept but would eventually like to try it with whole ge…
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I am trying to analyze tRNAs of non-model organisms (parasites) because I found out that Rfam doesn't include the tRNA sequences of my interest. I aligned all sequences of my interest and then tried t…
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Hi people,
I hope this is the right place to ask my question. If not, than please let me know an alternative. :)
I am kind of new in the world of whole genome alignments. I wanted to create a s…
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Instead of doing global alignment on whole genome sequences, align just the searched subtype ORF sequence to the full query sequence.
The searched subtype ORF sequence should be prefixed and suffix…