ncbi-sra,paired end dataset

Question

[sa1987]

hi

i have a rna seq dataset from ncbi.it shows paired end but only one sample is given under that sample.

how do we take this dataset? is there any error in the dataset?

please help

[MatthewP]

Do you mean only 1 .sra file? That's normal, if you download that sra file and extract you will see 2 fastq file for each end usually.

[sa1987]

Thank you for all the reply..i solved it ...i used ENA-EBI ..we can directly upload from ENA to galaxy

Answer 1

[Jianyu]

Usually, Read1 and Read2 are merged in sra file. You just need to add --split-3 parameter when using fastq-dump, the program will automatically detect the format and output two fastq files representing R1 and R2 reads if it is paired.

[ATpoint]

Agreed. Alternatively, you can directly download fastq files from the ENA (whichs mirros NCBI) as described here:

Fast download of FASTQ files from the European Nucleotide Archive (ENA)