minimap2 aligning sequencing reads to barcodes
Hi, I'm trying to demultiplex nanopore sequencing reads based on barcodes using minimap2 I find that when generating a sam file, the alignments have a TLEN of zero, does this mean there was no alignment? I can generate PAF files but only "secondary" alignments are given, no "primary" alignments. I will write a custom script to filter these to the best match based on number of matching bases but if there was a way to generate a PAF file containing only the best match that would be ideal. Any help welcome. Thanks, Matt
• 1,467 views
•
link
updated
by
GenoMax
•
written
by
matthew.tarnowski1 •
•
written
by
matthew.tarnowski1 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Understanding Re-use of Query Sequences in Long Read Alignments
written by Charles-Alexandre Roy •
-
vg giraffe handling of second vs. supplemental/split alignments, novel SVs, and associated MAPQ
written by Thomas •
-
Filtering for primary and secondary reads using sam flags (0 properly paired reads in alignment ste…
written by Marcel Glueck •
-
Which minimap2 parameters to set while performing mapping to avoid such mismatches
written by Mo •
-
Demultiplexing 10x fastq files by GROUPS of barcodes
written by bds1217 •
-
Understanding minimap2 output (PAF format)
written by Rogerio Ribeiro •
-
localised drops in read depth across sam/bam
written by matthew.tarnowski1 •
-
One read and One alignment
written by cxr5298 •
-
Single Cell Sequencing Quality
written by hsbinf •
-
Why Is Tophat Reporting Secondary Alignments Even When The Option To Do So Is Turned Off
written by Varun Gupta
Not answering your question but see if this helps: https://www.protocols.io/view/demultiplexing-nanopore-reads-with-last-7vmhn46
You should use
guppyto do the demultiplexing if possible.