minimap2

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Parameters for diploid ancient tetraploid

2

Hello, I have a phased assembly of a diploid organism. It happens it is also an ancient tetraploid (old genome duplication). I would like to show those alignments on a...

ghost

Calling large gaps in small contigs

2

Hi, I have somewhat short contigs in the range of 8 to 15 kbp. These contigs contain a 6 kbp insertion and are surrounded by 1 to 4 kbp of...

cgroza

this isn't an issue, rather a strange observation. I have mapped a set of genes on a genome assembly of the same species (but another lineage) using the option -ax...

rderelle

Hi Heng, I am using minimap2 to align CCS reads from cyclic DNA to a reference genome which is linearized. Here is my command: minimap2 -a -x map-ont --eqx -L...

lindongdo

First of all thanks hengli for making this tool. I used this tool to map long contig to ref genome. I noticed chain value is presented in tag fields. I...

yangyxt

produce gapless alingments

1

I am trying to get a gapless alignment of aligned sequences. Mismatches are fine, but I want to stop an alignment everytime there is a insertion or a deletion in...

HenrivdGeest

``` >7001174F:HCY5TBCX3200721:HCY5TBCX3:1:2202:11382:19258 0 19 39964932 51 7S8M1I77M * 0 0 CCCAGCCCCCAGCCCACAGCCCNCAGAGCTACCACCAGGTGGCGCCAAGCCCAGCAGGCTACCAGAATACCCACTCCCCAGCCAGCTACCACC IIIIIIHIIHIIGIIIIIIIIIFIIIIIIHHHCDIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIHHHIIIIIIIIIIHHIIIGIIIIIIII NM:i:2 ms:i:153 AS:i:153 nn:i:1 tp:A:P cm:i:8 s1:i:55 s2:i:0 de:f:0.0233 rl:i:0 Ref+: 1 CCCAGCCC-CAGCCCcCAGAGCTACCACCAGGTGGCGCCAAGCCCAGCAGGCTACCAGAATACCCACTCCCCAGCCAGCT 79 |||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Qry51:...

ruolin

Mapping transcripts to nanopore genomic reads

2

Hi, I use the following command to map transcripts to my individual nanopore genomic reads: `./minimap2-2.17_x64-linux/minimap2 -c -x map-ont -G4000 -F4000 -g4000 -r4000 --hard-mask-level -M 0 --secondary=no -uf -C5 transcriptome.fa...

chocotwig

I am running 2.17-r941 with the parameters `-ax splice -t30 -uf --secondary=no` In the first case, the following sequence is missing exon 1 (shown as soft-clipped) when aligned to mm10...

Magdoll

Reads not aligning when using mappy

1

I’m trying to use mappy for aligning 10 reads generated by MinION on Refseq database which is size of 177gb when indexed using minimap2. minimap2 aligns 9 out of 10...

samirdeshpande