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Hi Austin,
GMAP is an aligner that do not account for gene functionality (completeness, absence if STOP codons, frame-shift etc.). Just aligning the transcript sequence does not tell anything about…
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@jeizenga maybe you have some insight into this. I've spent the past day trying to figure it out from the side of the mapper itself and I'm now convinced that the problem is in the realm of the banded…
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Hi!
First of all, thank you a lot for providing this intriguing and well-documented piece of software.
I am working on an [experimental longread aligner](https://github.com/feldroop/floxer) and …
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Hi, Felix.
I'm so sorry to bother you again. I have WGBS data from the same batch for two species (Accel Swift data) and have already trimmed it using the method you suggested, with the following c…
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Hello,
I am glad to post about using the isaac4 aligner.
I am wondering that Isaac aligner --use-smith-waterman smart option.
--use-smith-waterman arg (=smart)
One of the foll…
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Hi Sir,
I got the same error after run both patch command (A & B): please suggest how i can solve the problem.
A. ragtag.py patch scaffold_RE2/ragtag.scaffold.fasta /media/d/D1/GBS_analysis/NGSE…
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The current `Alignment` struct for representing alignment results is defined as follows:
```rust
pub struct Alignment {
pub score: i32,
pub ystart: usize,
pub xstart: usize,
pu…
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Since `backtraceFrom` is implemented by recursion (instead of iteration), calling the aligner on "long" sequences (more than 1000 items) results in a `RecursionError` with Python defaults. Extending s…
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Hi,
I want to use criprVerse on a custom genome - a cell line- (no reference in public database like UCSC or NCBI)
I tried to adapt the tutorial "Design_Custom_Sequence" https://github.com/crisprVe…
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Hello Team,
parasail_aligner -a parasail_sg_qx_striped_32 -q SILVA_138.1_SSURef_tax_silva_prok_nr_sbsample_half.fasta -f Danish_01.fa -d -t 24 -g parasail.csv
for many sequences in query file…