easy way to assemble 50% of reads?

[gevielr]

Is there an easy way to separate a large fastq file of raw reads in half? I would imagine this should be pretty easy. I want to see how assembling half of my reads would do with some command... but I also have access to CLC and there doesn't seem to be a way to specify 50% of reads. This is a 70M+ 100 bp dataset.

[Patrick Dekker]

Hi,

Open the sequencelist switch to table view (5th icon below the sequences). Select a number of sequences and press "create sequencelist".

best
Patrick

[swbarnes2]

Use awk or grep or something to filter by the tile.

Or use unix head to get the top half of the file.

[jgibbons1]

If you know how many lines are in your file you can use the split command

$ wc -l file.fastq
100 file.fastq

$ split -l 50 file.fastq

[mbayer]

The head command in Linux also alllows you to extract a number of lines from the start of the file (or use the tail command for the end of the file), without splitting the whole file:

In analogy to the above:

$ wc -l file.fastq
100 file.fastq

$ head -n 50 file.fastq > halfAFile.fastq

cheers

Micha

[gringer]

The head command in Linux also alllows you to extract a number of lines from the start of the file (or use the tail command for the end of the file)

FWIW, there's also the split command:

split -n 2 file.fa file.split.fa. # for splitting a file into two

But bear in mind that raw reads from NGS runs frequently have low-quality reads near the start and end of the file, so you'll get a bit of quality bias from choosing a specific half of the file.