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no supplementary alignment in output

Open defendant602 opened this issue 5 years ago • 1 comments

Hi, ya dong: I use deSALT to align human ONT cDNA 1D reads to hg38 genome, but I find no supplementary alignments in the sam file.

This is my command: deSALT aln -t 40 -l 14 -s 2 -x ont1d -T index_dir fasta_file -o desalt.sam samtools view -f 2048 desalt.sam

But when I align the same data using minimap2, there are indeed supplementary alignments. I want to know how can supplementary alignments be reported by deSALT, since they are essential for fusion gene detection.

Thanks.

defendant602 avatar Jan 02 '20 02:01 defendant602

Hi, defendant: this is a good question which I have considered in my later work. But in the current version of deSALT, it can not output supplement alignments. In future work, a special SDP algorithm will be designed for fusion gene detection. So I am sorry for that, but if I have completed the function for fusion gene detection, I will remind you.

Best

ydLiu-HIT avatar Jan 03 '20 12:01 ydLiu-HIT