Unable to get unaligned files after HISAT2

Question

[s_bio]

Dear Community, We are trying to identify the viral transcripts in publically RNA-Seq datasets. This can be done by mapping the unaligned reads with the viral transcripts. However after using HISAT2 for alignment, though the alignment percentage is 76% but we are getting an empty unaligned file. The command that we are running is as follows:

hisat2 -p 24 --dta -x genome -1 SRR9593212_1_trim.fastq.gz -2 SRR9593212_1_trim.fastq.gz -S SRR9593212.sam --un SRR9593212_non_aligned.sam --summary-file SRR9593212_summary.txt
# 76% alignment rate
# getting empty SRR9593212_non_aligned_sam file

I would appreciate any help in this.

Answer 1

[iraun]

Hi! I noticed that you are providing the same file twice "SRR9593212_1_trim.fastq.gz", both when using -1 and -2, which might explain the issue.