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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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```
What steps will reproduce the problem?
1. choose a FASTA file with long headers as infile.fasta
1. run 'cd-hit -i infile.fasta -o outfile.fasta'
2. run 'cd-hit -i infile.fasta -o outfile2.fasta -d…
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Hi,
Can I extract the FASTA file of unmapped Sequences for later processing.
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I recently updated to framework commit `ca788d8941abc469ee6cac70daff3dfd67d9e47e` (engine commit `c9dda84396f287720d82249b0a1571e0ad9b6a82`) on the main branch and triggered a windows build of an app.…
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Hi,
I was trying to test run camisim using the docker image, but I ran into some problems. I tried a from profile simulation running metagenome_from_profile.py with the mini.biom file just as descri…
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**Steps to Reproduce**
1. Switch to macro mode
2. Select Snake mode
3. Open attached file [rna-mod-phosphate-example.zip](https://github.com/epam/ketcher/files/14360104/rna-mod-phosphate-example.zi…
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Split from #592, related directly to #1084
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We want to transition away from using AWS-iGenomes to using the central RefGenie server(s) to host reference genome assets for the nf-core pipeline…
ewels updated
2 years ago