extract subset of sequence

Question

[Björn]

Hi, How can I extract first 1 million lines or lets say first 250,000 reads (small rna) from xyz.fastq.gz file and export as a new file?

[noeD]

How to randamly extract reads from a FASTQ file?

or

zcat file.fastq.gz | head -4*#readYouWant > new.fastq

Answer 1

[cpad0112]

To extract first 250000 reads from xyz.fastq.gz (assuming that the said file has more than 250000 reads):

seqkit head -n 250000 xyz.fastq.gz > ouput.fq

Download seqkit from here. To count records in the output:

seqkit seq -n output.fq | wc -l

Output should be 250000.

[shenwei356]

just seqkit stats xx.fq.gz for counting.

it also support write gzipped file with -o out.fq.gz

[cpad0112]

thanks @shenwei356

Answer 2

[GenoMax]

Using reformat.sh from BBMap suite. reformat.sh in=original.fq.gz out=sampled.fq.gz additional_parameter_below

reads=-1                Set to a positive number to only process this many INPUT reads (or pairs), then quit.
skipreads=-1            Skip (discard) this many INPUT reads before processing the rest.
samplerate=1            Randomly output only this fraction of reads; 1 means sampling is disabled.
sampleseed=-1           Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
samplereadstarget=0     (srt) Exact number of OUTPUT reads (or pairs) desired.
samplebasestarget=0     (sbt) Exact number of OUTPUT bases desired.

Answer 3

[Pierre Lindenbaum]

Hi, How can I extract first 1 million lines or lets say first 250,000 reads (small rna) from xyz.fastq.gz file and export as a new file?

gunzip -c in.fq.gz | head -n 1000000 | gzip > out.fq.gz

[shenwei356]

pigz is recommended for faster speed.

[grant.hovhannisyan]

elegant:) one has to know there are exactly 4 lines for each read

[Pierre Lindenbaum]

t first 1 million lines or lets say first 250,000 reads (small rna)