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Hi,
I've updated the Debian packaging of sra-toolkit to version 2.7.0. The Debian build is running the test suite but unfortunately I needed to ignore some tests since these are failing. In this [pa…
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The `metadata` command should be followed by the `quant` command which isn't implemented yet. The command should look like:
`amalgkit quant --id SRR6337924 --fastp yes --threads 8 --ref Anolis_caroli…
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Hi,
I get an error running hamann, related to metaphlan, please see below.
**I use the following bowtie2:**
_64-bit
Built on
Sat Jun 6 20:17:22 UTC 2020
Compiler: gcc version 7.5.0 (cr…
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Hi,
I try to run the fungap pipeline, but each time maker 4 runs fails.
I installed the new FunGAP version and I update conda, I remove fungap environment and re installed all dependencies but it ke…
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Hello!
I have a question regarding fastq-dump and would appreciate your advice:
We want to download only a small subset of reads (5000 reads) from an SRA Run by using fastq-dump. We can use -N…
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Part of #2 but breaking this out as a separate issue for convenience. Identify a suitable dataset to use for testing and validation purposes for the short read alignment pipeline.
* [x] fastq seque…
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**[Data Retrieval](**url**)**
NCBI’s fastq-dump from sra-toolkit was used to download the short reads for NCBI short read archive (SRA).
#Using SRA-toolkit
```
prefetch SRR292678
fastq-dump …
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**[Data Retrieval](**url**)**
NCBI’s fastq-dump from sra-toolkit was used to download the short reads for NCBI short read archive (SRA).
#Using SRA-toolkit
```
prefetch SRR292678
fastq-dump …
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This issue is to address a problem with installation reported by @carolynePearl in two other threads:
- https://github.com/sunbeam-labs/sunbeam/issues/205#issuecomment-525664406
- https://github.c…
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Hi,
can I use Fungap without the Illumina paired-end mRNA reads files?
I have only the genome assembly.
Thanks.