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BCALM doesn't crash nicely when the input is an incorrect fasta file. The current error message is:
```
>cat blin.fa
adfad
> bcalm -in blin.fa -kmer-size 3
BCALM 2, git commit e9ba83c
setting st…
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From this:
https://groups.google.com/a/lbl.gov/forum/#!topic/apollo/vTNqtZSfl5M
The basic idea would be to allow an export option where the output FASTA would be re-assembled within Apollo, inst…
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Fasta sequence headers may contain additional text after the first whitespace, but this is not considered part of the sequence ID. When converting such a file (e.g. to relaxed phylip or nexus) this te…
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Currently ``02-sequence_databases/04-programming_for_web_blast.ipynb`` and ``03-lipases/XX-runthrough.ipynb`` use this pattern for calling QBLAST:
```python
result_handle = NCBIWWW.qblast("blastx"…
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I got the following error (when using MSGFPlus through OpenMS' MSGFPlusAdapter)
```
java.lang.ArrayIndexOutOfBoundsException: 1
at edu.ucsd.msjava.msdbsearch.CompactFastaSequence.getByteAt(Compa…
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# Background
Ziv lab needs to switch the genome reference file for their needs. The first step this comes in to the pipeline is the BWA alignment step.
# Task(s)
Make it possible to change the g…
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Hello,
I'm running 'poreseq extract' to get the sequence out a folder containing the fast5 files. I get no sequences extracted getting the message 'Done, extracted 0 2D fasta sequences'. I have che…
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Dear @cjain7 ,
When I mapped the ONT reads to GRCh38 without alt sequence using winnowmap with version 2.0.3, it occured the warning message just like "failed to parse the FASTA/FASTQ record next t…
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I was wondering if I can generate a MAF (mutation annotation file) from a Fasta file which contains the consensus sequences of multiple samples. I ask, because I wanted a best way to define when mutat…
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Just wanting to give the package a try and I'm having a hard time getting past loading the example data. I'm getting this error in Biostrings -- might not have to do with the `mmgenome` package, but …