Tips and Tricks for working with Remote Computers

Use screen to run things that take a long time.

Often you want to run things that will take days or weeks to run. The ‘screen’ command will let you run programs and record the output, and then come back later and “reconnect”.

(See Using ‘screen’ for instructions.)

Use CyberDuck to transfer files

To transfer remote files to your local laptop, or local laptop files to the remote system, try using CyberDuck.

Subsetting data

If you want to generate a small subset of a FASTQ file for testing, you can do something like this:

gunzip -c /mnt/data/SRR534005_1.fastq.gz | head -400000 | gzip > sample.fq.gz

This will take 400,000 lines (or 100,000 FASTQ records) from the beginning of the SRR534005_1.fastq.gz file and put them in the sample.fq.gz file.

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