xiekunwhy

python -m jcvi.formats.gff fixpartials cost huge memory.

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Hi, Why python -m jcvi.formats.gff fixpartials cost huge memory? Gene number in gff file ~30000(~60000 mRNA, ~19000 are partial). And genome fasta 1.3G  Best, Kun

Hi, I use mmseqs2 to align genome sequences, but I found that the alignment length are always smaller than 10kb. Here are the steps describle how I use mmseqs2 1)...

BLAT-like search

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## Expected Behavior Is it possible to use mmseqs2 to do BLAT-like search or give result format like blat (https://genome.ucsc.edu/cgi-bin/hgBlat), how to do that if it is possible? Best, Kun

Input AGPs do not have the same set of components

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Hi @malonge , I open a new issue to report ragtag.py merge errors (mentioned here https://github.com/malonge/RagTag/issues/66 ), and I have sent you an e-mail using [email protected]. Best, Kun

Hi, Is it necessary to sort bam files by read names before markdup? Best, Kun

We need to run tirvish two times for a single genome?

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Hi, We need to run tirvish two times for a single genome (one run for original sequence and an other run for reverse complement sequence)? I found some describtions here...

There is no -retainids when using ltrdigest, Why don't add one?

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Hi, I found that all IDs were changed after running ltrdigest, why don't add -retainids option to retain original IDs like sort and select? Best, Kun

Can we use megahit to assemble rna-seq data?

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Hi, Can we use megahit as a denovo assembler to assemble rna-seq data? Best, Kun

Hi, I am looking for some assemblers to assemble a high heterozygous rate plant genome(diploid, het rate > 2%, haplotype genome size ~3.6G). And I want to know how to...

Are there some option to reduce temporary vcf file number?

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Hi, It seems that octopus open one temporary vcf file per contigs/scaffolds. For many non-model species, there are many contigs/scaffolds in their reference genome, for example https://www.ncbi.nlm.nih.gov/assembly/GCA_000966675.2/ , the number...