Hello all. I have .fastq files but with many reads/lines , how can i reduse that number f.e. 10000 lines and get a new file? Only using the terminal, not with some program ( macOS ). i would like a way that i can use any type of file and be able to reduse to whatever number
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dimitrischat
You can use sed to remove lines from a file (which is what I think you want?). The following command removes lines 45000-55000 from yourfile.fastq and saves the result in a new file called shorterfile.fastq:
sed -e '45000,55000d' < yourfile.fastq > shorterfile.fastq
Or you can use head or tail to extract the first (head) or last (tail) number of lines from a file, e.g.:
head -n 10000 yourfile.fastq > newfile.fastq
The BBMap package has a tool called Reformat which can do this:
reformat.sh in=file.fastq out=reduced.fastq samplereadstarget=10000
That will sample 10000 reads randomly from the file. It can also process paired fastq files at once (with the in1 and in2 flags), keeping pairs together.
split https://linux.die.net/man/1/split
see also : Split Fastq File In Small Fastq Files - Windows splitting fastq files output size issue
the first link is about splitting, i want to select the first x lines from the fastq file
If you are going to sample reads then I suggest not selecting first "x" reads from a file. Those reads may represent bad parts of data since they would be starting at the edge of the flowcell. With old(er) Illumina data a lot of the initial reads in a file used to have N's/bad Q scores.
In my experience, they still do... :)
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I had answered this question yesterday in a different thread posted by OP: C: tophat 2 rna seq