Merge branch 'sratoolkit' into 'master'

Update documentation for Sratoolkit

See merge request !311

content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/sratoolkit.md

@@ -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 %}}