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Other formats work, but not phylip for some raisin:
```
josephwb@Potiphar-Breen:baits$ cat foo.fa | pxlssq
File type: fasta
Number of sequences: 4568
Is aligned: true
Sequence length: 2571
----…
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Can you please explain the values in the final vcf file, especially for ALT and INFO columns?
#CHROM POS ID REF ALT QUAL FILTER INFO
1 726104 1:726104:FP A A[COMPONENT_947_a_length_353_size_5f:135…
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Hello,
I would like to use racon to error-correct chloroplast (a subset of all reads, made by aligning all reads to the assembly containing cp contigs) PacBio CLR reads and I keep running out of memo…
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I noticed that the collaborators are using the somatic VCF files to look for somatic mutations in the HLA genes. These genes are known to be problematic for alignments to the human reference genome si…
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Hi, I'm an undergraduate researcher in UW and I'm quite interested about how to construct the "optimal sequence" for each year based on the historical data "H3N2_HA1_all_years_filtered.fasta", which i…
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```
What steps will reproduce the problem?
1. Build genome and reads .DAT files
2. Make jump databases
3. Attempt to align ~5M reads to the genome
What is the expected output? What do you see instead…
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Hi,
An error (OSError: [Errno 28] No space left on device) occurred when running exonerate.
I checked my device, it looks like there is plenty of space left.
Filesystem Size Used Avail Use…
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see #136 for an example description. Doesn't have to be much, but ideally should include the version of the genome assembly and what the annotations are/where they are from for a genome, and what is …
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## Platform
- SeqAn version: 3.3.0
## Question
Is there a documented way to extract, from a pairwise alignment result, the alignment slice positions (equivalent to the coordinates[] list of…
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Like length and/or repetitiveness