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Hello, we are keen to use MITE-Tracker on our insect genomes (size=300Mb, diploid genome). We tested the tool on a genome, expecting the run to be as short as the rice genome example of the BMC Bioinf…
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from version v0.0.18 we start to infer the genome size for peak calling from the provided genome file, before we set this using instead of using macs available defaults.
This changes the background …
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Dear PGGB team,
I have a few questions about your great program.
Based on the program, it appears that wfmash performs all-vs-all alignment on a single node. From my trials, this is indeed the c…
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Thanks for the GenomeScope tool, we have used it successfully for several genomes we have assembled. Now we are trying to determine the genome size of a spider. Spider genomes can be as small as 0.8G …
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Hi, I can generate genome from STARconsensus pipeline using this command
```
STAR \
--runThreadN 15 \
--runMode genomeGenerate \
--genomeDir $star_genome_outdir \
--genomeFastaFiles $ref_fasta…
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Hi,
I have been trying out scaffolding the pacbio contigs using scaff10x, using the latest version the version 4 uploaded last month.
I can see that the align* series files are empty, but the to…
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as of the merge of #160, charcoal now performs the following steps -
1. find candidate genomes for contamination analysis, based on sourmash shared hashes with GTDB r95
2. download genomes and per…
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Hi!
I have used hifiasm(0.14-r312) on HiFi-reads only to assemble an allotetraploid plant(coverage ~50x). The options : -t48 -l0 were used in this assembly. All output files were generated successful…
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Hi Jiekai Lab - thank you for developing such great resouce!
I keep on having an issue to create custom genomes for scRNA analysis. Even when I run the example data with:
scTE_build -te ./Data/TE.…
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Hello, first thank you for developing such great tools
I am Ruba PhD student in Germany and I am doing scRNAseq analysis for my data, I wanted to check the velocity and so I generated the loom files …