Question: How to randomly subset a specific number of sequences from a large fastq file?
0
gravatar for j.thomas93
13 months ago by
j.thomas930
j.thomas930 wrote:

Hi,

So I am doing some RNA seq and I have a number of large library preps for the different conditions and replicates. In some samples there a huge differences in library size and I was hoping to just do a preliminary analysis where I randomly subset x amount of reads from the parent fastq, but i want to do it multiple times from the sample fastq to generate a more representative sample. I need the sampling to therefor be random and different for each subset

Is this possible?

Thanks in advance for any help

rna-seq tool • 508 views
ADD COMMENTlink modified 13 months ago by benformatics1.6k • written 13 months ago by j.thomas930

Also seqkit sample by specifying --number or --proportion.

ADD REPLYlink written 13 months ago by SMK1.9k
2
gravatar for benformatics
13 months ago by
benformatics1.6k
ETH Zurich
benformatics1.6k wrote:

Please use the search function before posting a question.

ADD COMMENTlink modified 13 months ago • written 13 months ago by benformatics1.6k
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