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2.2 years ago
s_bio
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10
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.
