Questions tagged [minimap2]
The minimap2 tag has no usage guidance.
18
questions
1
vote
0
answers
47
views
java.lang.ArrayIndexOutOfBoundsException: Index 86 out of bounds for length 86
I use the next versions:
gatk 4.4.0.0
minimap2 2.26-r1175
samtools 1.19
I have a fastq file. And try to implement gatk MergeBamAlignment to generate a new ...
- 2,464
5
votes
2
answers
240
views
Why are Minimap2 alignments different with CIGAR generation flag?
I am using Minimap2 (v2.26-r1175) in Linux to generate a sequence alignment between the Streptomyces coelicolor A3(2) chromosome (ref.fa) and the Mycobacterium ...
- 221
0
votes
1
answer
131
views
Is my reference sequence too small?
I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
- 1,053
1
vote
2
answers
586
views
Parameter optimisation of minimap2
I'm leveraging minimap2 to map select genes from short-read microbial fastq metagenomics zip files.
...
M__♦
- 12.8k
2
votes
0
answers
267
views
Extracting positions from PAF files in order to extract sequences from a Fastq file with Python
I have used Minimap2 to create a paf file by aligning a Fastq file against itself. Now from this Paf file I can see where the reads overlap, and I want to take these positions, and use them to extract ...
- 10.5k
2
votes
1
answer
1k
views
Understanding PAF format
Does anyone have any experience with PAF files (minimap2 output)? I don’t fully understand what my output means.
I’ve looked at the minimap2 explanation (https://github.com/lh3/miniasm/blob/master/PAF....
- 14.9k
1
vote
1
answer
344
views
Nextflow with Minimap2 not working
I'm trying to create a Nextflow script that maps assemblies to reference gene sequences. This is what I have so far:
...
- 14.9k
3
votes
1
answer
2k
views
Why index a sequence file with minimap2?
I have been using minimap2 for a few month now and I just found a script that follows these steps:
...
- 1,759
2
votes
1
answer
255
views
Get number of reads with a single, (almost) exact match to the full length of a reference sequence
I can't find an answer to this in previous questions, so hoping someone can help me now.
We have nanopore sequenced a PCR product, and I've filtered our reads to +/- 10 bp of the expected product ...
- 14.9k
2
votes
2
answers
5k
views
How do you visualize minimap2's PAF output format?
As described by the developer of minimap2:
PAF is a text format describing the approximate mapping positions between two set of sequences.
He also suggest to use either Ribbon to visualize PAF files,...
- 175
3
votes
2
answers
219
views
Minimap2 detects too many 16S sequences in metagenome
I'd like to extract bacterial sequences from a metagenome where ~99% of contigs are from a host insect. My current protocol minimaps every 16S sequences present in the sample, then blasts all those ...
- 6,575
1
vote
1
answer
106
views
How to plot the gap distribution of contigs wrt to reference genome
I have a contigs file that I generated using Minia and then I have used Minimap2 to map these contigs again to the reference genome. Now I want to plot the gap distribution i.e. gap distance of the ...
- 4,212
3
votes
1
answer
3k
views
Convert PAF format to SAM/BAM format
I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use ...
- 81
2
votes
1
answer
680
views
What do the symbols mean in minimap2's gap cost equation?
Heng Li's paper on minimap2 is understandable to me right up until the moment that it gives this definition of gap cost:
2.2.1 Alignment with 2-piece affine gap cost
Minimap2 performs DP-based ...
- 155
4
votes
2
answers
463
views
Mapping Reads to Known Gene Paralogs with Long Read Technology
I have some sequencing data from a captured region that is a known paralog edited. For now, I have been mapping the data using standard minimap2 flags for PacBio DNA sequencing:
...
- 631
4
votes
1
answer
252
views
Error correction within the long read
I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What is done in the lab is the following:
The plasmids are purified by size.
We amplify the plasmids using the ...
- 143
3
votes
2
answers
741
views
How to map reads shorter than 32bp with minimap2?
I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
- 6,575
2
votes
1
answer
242
views
Minimap2 -ax map-pb doesn't output tlen field
I have used minimap2 to map some pacbio reads to a reference genome. I would like to know the "insert size" (true length of sequence) relative to the reference. More specifically, I want to know the ...
- 19.8k