Commit 5f8fb9ef authored by Natasha Pavlovikj's avatar Natasha Pavlovikj
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Merge branch 'sratoolkit' into 'master'

Update documentation for Sratoolkit

See merge request !311
parents 15b5e8ed d9d71979
......@@ -44,6 +44,15 @@ fastq-dump --split-files input_reads.sra
{{% /panel %}}
This script outputs two fastq paired end reads `input_reads_1.fastq` and `input_reads_2.fastq`.
To download `bam` files from NCBI using the SRA identification, the following commands can be used:
{{< highlight bash >}}
$ module load SRAtoolkit/2.11 samtools
$ sam-dump <sra_id> | samtools view -bS - > <sra_id>.bam
{{< /highlight >}}
where `<sra_id>` is the assigned SRA identification in NCBI (e.g., SRR1482462).
All SRAtoolkit commands are single threaded, and therefore both `#SBATCH --nodes` and `#SBATCH --ntasks-per-node` in the SLURM script are set to **1**.
......@@ -64,3 +73,7 @@ Other frequently used SRAtoolkit tools are:
- **vdb-encrypt**: encrypt non-SRA dbGaP data
- **vdb-decrypt**: decrypt non-SRA dbGaP data
- **vdb-validate**: validate the integrity of downloaded SRA data
{{% notice info %}}
**If needed, the location of the caching on a per-user basis can be changed with `vdb-config -i`.**
{{% /notice %}}
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