Estherrr1997

CIGAR and query sequence are of different length after mapping

1

Hi, I am using minimap2-2.24_x64-linux for mapping genome assemblies. After mapping them with minimap2 I would like to convert the sam output to a bam output, when I try this,...

Hi there, I have installed Dotplotly and I try to run it using my data but I get this error (the same error occurs when running dotplotly on the example...

error creating dotplot

13

Hey there, I am trying to create a dotplot of an alignment I made with minimap, I converted the minimap output (sam format) to a paf format and tried running...

Orthofinder does not run further than blast

2

(blauwe_haai) kockelmans.e@localhost:/exports/nas/kockelmans.e$ orthofinder -o orthofinder_test_2 -d -f orthofinder_files/ /home/kockelmans.e/.conda/envs/blauwe_haai/lib/python3.9/site-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.16.5 and orthofinder_test_2/Results_Sep07/WorkingDirectory/Blast1_2.txt.gz Command: blastn -outfmt 6 -evalue 0.001 -query orthofinder_test_2/Results_Sep07/WorkingDirectory/Species1.fa -db orthofinder_test_2/Results_Sep07/WorkingDirectory/blast_nuclDBSpecies2 | gzip > orthofinder_test_2/Results_Sep07/WorkingDirectory/Blast1_2.txt.gz...

set xpos per species

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Hi, I am using the SankeyNetwork function of D3Network. I was wondering, does NetworkD3 has a function to set the xpos for a set of nodes? I am using a...

Can't read dotplot results

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Hi there, I created a dotplot with pafR to compare large genomes, altough I can't really read the dotplot since the lines of the figure (the raster) makes it hard...

Hi there, I am using minidot to plot genome assemblies. I already mapped the assemblies using minimap2 and I would like to visualize the results using minidot. Although I seem...