Low alignment rate using fastq files obtained from SRA

[cdiazmun]

Dear,

I'm experiencing some issues when running bowtie2 on a set of samples obtained using fastq-dump SRR012345678. I used the following command: bowtie2 -x reference_genome -U sample.fastq -S sample.sam -p 12. Since fastq-dump only ouputs a fastq file, I assumed I had to use the -U option. I also tried setting the -1 and -2 directed to the same sample.fastq (just to see what happened), and the alignment rate is practically identical, almost 0 %. Should I process further the fastq reads obtained with fastq-dump before inputing them to bowtie2?

[cdiazmun]

UPDATE:

I mapped the same sample to the same reference genome using BWA and it mapped 94,6 % of the reads, albeit 99,2 % of them were supplementary alignments.

[cdiazmun]

UPDATE2:

Everything is solved by adding the flag: --split-3 when running fastq-dump, so that the paired forward and reverse reads are separated and can be read by Bowtie2 accordingly. 93.55 % of alignment rate and 0% of them as supplementary alignments. I, therefore, close the issue.