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Is it possible to let kmc read sra files?
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In order to better promote reproducible research, aroma.seq should report on versions of external tools it uses. As a started this should be easy to add for verbose output messages, but ideally it sh…
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## Large usage MD codes
- [ ] [LAMMPS + variants](https://github.com/UCL-ARC/hpc-spack/issues/44#issuecomment-2179076165): https://github.com/UCL-RITS/rcps-buildscripts/issues/575
- [ ] CP2K: https:/…
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This misbehavior happens with fasterq-dump 3.0.7 on the following accession and a few others, at a rate of about 7% of biosample-based accessions. **SAMN08049698** and some other biosample-based acces…
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Hello,
I downloaded some sc data from a public repository (generated with Chromium Single-Cell 3′ Gel Bead and Library V2 Kit). The issue here is that the fastq file contains only one read where R1…
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Hi,
I'm attempting to download some scRNAseq files from SRA, and convert them to fastq.gz format to use as input to CellRanger.
I am using sratoolkit v2.10.8.
This is an example of one of the f…
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In some of our WGS datasets, SeqSero2 (`v1.1.1` using the default microassembly approach) returns **O2** or **O9** seemingly at random:
| Sample | Predicted antigenic profil…
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### # Downloads input files:
### #Known variant file
`[wget ftp://ftp.ensembl.org/pub/release-99/variation/gvf/homo_sapiens/homo_sapiens-chr18.gvf.gz' -O homo_sapiens.vcf.gz](url)`
# # Select varia…
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I am trying to download phenotype files from dbGaP, and the phenotype files are failing. I have downloaded a couple SRA read files to confirm that the prefetch utility is working - only the phenotype …
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for
```
~/sratoolkit.2.8.1-3-ubuntu64/bin/fastq-dump.2.8.1-3 -A SRR1929297 -Z | syrah -k 31 | sourmash compute - -o SRR1929297_syrah.sig
```
```
syrah!
reading sequences and outputting soli…