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Hello,
I ran hifiasm on my pacbio Hifi raw data with the following command:
hifiasm -o it20_007_hifi.asm -t 40
Before I made a genome size and heterozygosity estimation of my raw data…
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I've used Racon on > 200 assemblies and have only had this error arise with one sample...
The reads in this case are ONT reads that I mapped to my assembly using Minimap2. The coverage distribution…
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Hi,
I have been using minimap2 for many genome to genome alignments and I have noticed an odd pattern.
If I take a large genome like a human genome and align (paf output) the whole chromosomes …
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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 flanking reference sequence on each side. I wish to use mi…
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```
I ran msatcommander on two files of contigs from two different assembly
programs (using the same data) and was returned the same number of searched
contigs (65536) there were however more in one…
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splay outputs across more directories to mitigate performance problems having to do with large numbers of outputs.
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Hi Mahmoud,
currently, I am testing JAMM on GRO-seq (SE protocol, Pol2 ChIP-like pattern) in dm6. This genome version contains a lot of small contigs, which I'd like to ignore/exclude from being an…
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The purity stats with MUMmer don't work well with circular or fragmented genomes, because a perfect alignment is actually split up into multiple different alignments.
See also:
http://nbviewer.ipyth…
inodb updated
10 years ago
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Hello,
I have a question about how the VDJs are assigned to the contigs.
I have a trust4_cdr3.out, and I can see for example for malignant cells in my data, there are multiple VDJs. How is this po…
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When I assemble PacBio HiFi reads of a Eukaryotic linear genome through HiFiasm, I get a couple of circular contigs. The linear contigs are appended with an `l` in the fasta header, and the circular c…