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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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prevent read splitting/clipping #60

Open gvic628 opened 5 years ago

gvic628 commented 5 years ago

I used NGMLR to map minION long read data back to a reference genome. May reads are split/clipped. Is there an easy way to view the reads that were clipped? Is there any way to prevent the NGMLR algorithm from splitting/clipping reads so that only the reads that are a precise match to the genome region in question are mapped?

fritzsedlazeck commented 5 years ago

You can view them in IGV. Are you mapping against a reference genome our an assembly? There is currently no parameter to completely deactivate the clipping/ splitting of reads. Thanks Fritz

gvic628 commented 5 years ago

Hi Fritz, Thanks so much! I am mapping the reads against both a de novo long read assembly (based on ONT data) as well as a reference genome downloaded from JGI.

fritzsedlazeck commented 5 years ago

So for a de novo assembly, it is normal to see many reads clipped. Especially if its not polished. This is because you have the raw sequencing error + the errors in the assembly as a difference. For the reference genome that should improve. Thanks Fritz

YichaoOU commented 3 years ago

Hello,

Is there a good way to visualize these clipped reads? If I visualize the bam file in IGV, since the same read is split into multiple alignments, I can't easily see the deletions.

Thanks, Yichao