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#1825 added support for alignments, which passed through arguments for supporting missing data to the haplotypes method. However, the initial implementation was wrong. Consider the following example:
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For some applications, such as protein-RNA complexes, I'd like to pair sequences by a custom method- and input already paired seqs (2 alignments where sequence X in ali 1 is paired with sequence X in …
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Hi,
I'm curious as to why to different samples using the same GTF file have different content in the fromGTF.*.txt files. I was on the impression that this was the ensemble of alternative splicing…
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I deal a lot with core genome SNP alignments (DNA) across 100s of bacterial samples. A useful report would be like this:
```
ID #A #G #T #C #N #-
aln1 12 31 11 31 0 8
aln2 11 44…
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I've been running the 241 mammal genome alignment from Zoonomia (https://cglgenomics.ucsc.edu/november-2020-nature-mammalian-and-avian-alignments/) through a few different filters now. When I get to t…
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Hi Paul,
Amazing software!
I have several questions about the HyDe. I see the input data should be diploid data or ambiguous sites. But here I have a diploid species and tetraploid species, an…
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This is the commands I entered:
RNAEditingIndex \
-d /fs/project/PAS1348/Software/RNAEditingIndexer/TestResources/BAMs \
-f _with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam \
-l /fs/pro…
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Hi,
I exported axt format files through lastz(human as ref) genome comparison and obtained many pairwise alignments files(Each file is a human reference, e.g Homo_sapiens-Lemur_catta and omo_sapien…
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Hi,
I was using miniprot to align one protein in Sorghum to maize genome, but no matter how I changed the parameters, only one alignment was returned. But if I used tblastn with default parameter, …
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I try to use CONDA environment and manually install pasa, but in the manual installation, because it is a non root user, the software that pasa depends on is installed with CONDA, only the pasa softwa…