I am using fasterq-dump for obtaining fastq files. Some of the experiments corresponding to GSM ID are containing multiple SRR ID´s. e.g.

GSM ID https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2534657

SRA Run selector https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRX2636516 contains 3 SRR ID SRR5339574 , SRR5339575, and SRR5339576.and fasterqdump I got one (single-end) fastq file for SRR533957, whereas other remaining two are paired-end fastq file. What is possil

fasterq usage

fasterq-dump SRR5339574 -F --skip-technical --split-3 -O/fasterq-output

I tried to find documentation about whether these fastq files from multiple runs are merged for alignment. How to merge SIngle-end and Paired-end fastq files together how to do perform alignment using e.g BWA-mem.

Thanks in advance

ank