minimap2

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Single base exon in splice alignment

1

I have a long read (ONT) that I am aligning to the reference genome using Minimap2 `-x splice` mode. Minimap2 is generating a 1bp exon as part of the alignment...

baraaorabi

Adjusting penalty scores in the miniprot splice model

1

For minimap2 (versions 2.25 and above), it seems like the miniprot splice model is used for aligning RNA-seq reads by default. According to the miniprot paper, there are fixed penalty...

RNA-ROB

unexpectedly low depth of coverage after mapping with MiniMap2

3

Hello, I have 3 samples I'm working with. By comparing the total ONT sequenced read length and the estimated haploid genome sizes sample 1: 24.96x coverage sample 2: 22.36x coverage...

sjfleck

Hi all, I am analyzing the nanopore sequencing data for thalassaemia cases for which gene duplications were suspected. Anyone know how to set minimap2 parameters for this kind of alignment...

Jinglu1982

I am currently using minimap2 (v2.24) with the default alignment settings for aligning scaffolds, contigs, and Hifi reads. However, I have come across a peculiar observation. While aligning contigs, instead...

justdx

hi，I met some very strange problems.When I ran minimap2, it worked normally at first, but after I successfully processed several files, it had such a problem. ``` minimap2 -ax sr...

Maxwell-codesome

Can I distinguish read1 and read2 from the PAF format output?

1

Hi, When I map short paired reads but don't want to output sam format files, can I distinguish read1 and read2 in PAF file? ``` minimap2 -x sr ref.fa sample_R1.fq.gz...

silvewheat

Hi, I have sequenced some RNA with a flowcell and I got around 2M reads. I tried to align them to the human transcript (https://www.gencodegenes.org/human/) . However when I use...

matjack2000

Hi, I want to align the assembled sequence (HJ.stLFR_CCS.maternal.fasta.gz HJ.stLFR_CCS.paternal.fasta.gz) to the human HPRC reference sequence (HPRC.Phase1.CHM13v2_Non-W.gfa) using the following command. The final GFA output (out.gfa) is smaller than the...

GeorgeBGM

How to choose args If the deletion is close to the edge of a PCR ampify read

3

minimap2 requires long enough flanking regions to bracket a long indels. Without this requirement, there will be more false positives. If the deletion is close to the edge of a...

cherryamme