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18 changes: 16 additions & 2 deletions computing_tips.md
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Expand Up @@ -17,8 +17,22 @@
* Change the configuration setting
* Add jupyter kernel with `ipykernel`

## SRA/fastq at EBI database
* Ruiyan add more links
## How to download raw fastq file
* Method 1 : `prefetch $SRA_ID` & `fastq-sump --gzip`
* Method 2 : Search the SRA_ID in EBI database & download by using `axel`
* Method 3 : Search the SRA_ID in EBI database & download by using `ascp`
Example code:
```bash
#!/bin/bash

for i in {51..52}
do
echo $i
ascp -QT -l 300m -P33001 -i /home/houruiyan/.conda/envs/Py3/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR116/0${i}/SRR116539${i}/SRR116539${i}_1.fastq.gz .
ascp -QT -l 300m -P33001 -i /home/houruiyan/.conda/envs/Py3/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR116/0${i}/SRR116539${i}/SRR116539${i}_2.fastq.gz .
done
```


## Misc
* Python module auto reload [links ?]
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