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Hello Biologger - your prior suggestion for Issue 15 was great and solved the problem I was running into. However, now when I run the version of the pipeline you suggested, I get the following error:
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I run this command with the new version of magnet
`python magnet.py -i ZYMO_D6311_14.nanoq.10.1000.fastq.gz -m ont -o ZYMO_D6311_14.magnet_1 --threads 30 -c relative_abundance.tsv`
i get this error
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Hi,
I'm encountering an issue while mapping some samples using STAR. The process begins normally and successfully maps the first sample, but then the subsequent samples are ignored. When I attempt to…
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Hello again,
I was trying to align the corroboree frog and _X. tropicalis_ genomes. The corroboree frog genome ([GCF_028390025.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_028390025.1/)) i…
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Extrapolated from common sequencing targets from the SRA, and sequences that returned false positives during initial database screenings:
- Human genome - integration sites: https://hgdownload.soe.…
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Hi All - having many jobs fail with this type of error, which seems to indicated perhaps something about a poorly formatted fasta file? One issue is that I can't seem to find the offending file `GCF_0…
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Assignment instructions:
- [x] Align the reads to hg19 build 37 genome
- [x] Generate quality statistics from the fastq or bam file using your tool of choice.
- [x] Call variants for the regions in…
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### Is there an existing issue for this?
- [X] I have searched existing issues, it hasn't been reported yet
### Use case description
wanted to deploy google cloud function [2nd generation](https://…
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Hi, I would like to know how STAR usually handles highly variably gene sequences like V(D)J sequences that code for parts of the TCR / BCR (T-cell and B-cell receptors), please?
I guess it depends …
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When I used LRA to align the HG002 ONT data and ran the following code, I did not get any results. However, other alignment software worked fine.
```
/home/xxx/00.Software/SVDSS/SVDSS_linux_x86-64 i…