How to download the final reads of SRA data from NCBI using fastq-dumb

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3.5 years ago

FadyNabil ▴ 20

Say I have an SRA data file that contains many reads I want to use fastq-dumb to download the final for example 5 reads from this file

fastq fasta SRA • 1.1k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 3.5 years ago by FadyNabil ▴ 20

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The command that works for most cases is:

fastq-dump --split-files [SRR ID]

ADD REPLY • link 3.5 years ago by Kevin Blighe 88k

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I do not want to split I want to download for example the final 5 reads to check the quality of this data using fastqc

ADD REPLY • link 3.5 years ago by FadyNabil ▴ 20

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Five reads are not enough for a QC. Download everything and run through fastqc. The split option is important for paired-end data..

ADD REPLY • link 3.5 years ago by ATpoint 85k

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the fastq-dumb makes my day, you can check the help for the tool https://ncbi.github.io/sra-tools/fastq-dump.html

ADD REPLY • link 3.5 years ago by JC 13k

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