How to extract paired-end reads from SRA files(reprint)

SRA(NCBI) stores all the sequencing run as single “sra” or “lite.sra” file. You may want separate files if you want to use the data from paired-end sequencing. When I run SRA toolkit’s “fastq-dump” utility on paired-end sequencing SRA files, sometimes I get only one files where all the mate-pairs are stored in one file rather than two or three files. The solution for the problem is to always run fastq-dump with “–split-3” option. If the experiment is single-end sequencing, only one fastq file will be generated. If it is paired-end sequencing, there may be two or three fastq files. Two files (with suffix “1” and “2”) are matched mate-pair read file where as the third one (without any suffix) contains all the reads that do not have any mate-paires (or SRA couldn’t resolve mate-paires for them).

Hope my experiences with NCBI SRA data handling help the readership.


SRA toolkit document:

An example command:

./fastq-dump.2 –split-3 ~/Desktop/ERR068552.sra -O ~/Desktop/temp.fastaq/

PS: 如果测序使用的是ligation,结果为2 base encoding的color-space reads,可以加入-B选项使得fastq中的序列为base space reads


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