biser

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Hi there, thanks for providing this excellent tool. I have some questions about the `biser` output results. - There are some SD mates with very close genome distances. Does `biser`...

IvanWoo22

how to get those information from the output of Biser ?

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uint indelN; "number of indels" uint indelS; "indel spaces" uint alignB; "bases Aligned" uint matchB; "aligned bases that match" uint mismatchB; "aligned bases that do not match" uint transitionsB; "number...

Shuixin-Li

ERROR: BISER failed (-11):

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I have a question： ERROR: BISER failed (-11): [p] /public1/home/scb4191/miniconda3/envs/biser/lib/python3.8/site-packages/biser/exe/biser.exe search /public1/home/scb4191/Gall-aphid_genome/SDs_analysis/MB.genome.mask.fa -c ptg000042l -o /tmp/biser.tucjvlg9/search/MB.genome.mask_ptg000042l_0.bed 0 --kmer-size=14 --winnow-size=16 --max-error=0.3 --max-edit-error=0.15 --max-chromosome-size=300000000 Thanks a lot

WHY0929

Whether the number of contigs affects the efficiency of BISER

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Hi, First, thank for you tools. I run the `biser` on a genome assembly with 25 chromosome-level scaffolds and 1983 short contigs (the longest contig is ~ 300kb and the...

life404

ask for help, the ERROR: BISER failed (-9):

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Running BISER v1.4 on 1 genome(s): hap1_map_cs10_id 0. Hard-masking genomes Hard-masking: 00:41s (single: 00:36s) 1. Putative SD detection ERROR: BISER failed (-9): [p] /public/home/zhangjiangjiang/anaconda3/lib/python3.10/site-packages/biser/exe/biser.exe search /tmp/biser.9neoobgd/genomes/hap1_map_cs10_id.fa -c Chr06 -o /tmp/biser.9neoobgd/search/hap1_map_cs10_id_Chr06_0.bed...

Jiangjiangzhang6

Hi inumanag, We would like to express our sincere gratitude for developing this excellent tool. Now, we aim to determine whether a pair of paralogous genes (geneA and geneB) are...

baoyutao1

python -m biser -o Chr2.bed --max-error 0.2 --kmer-size 1000 -t 10 Chr2.fa

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Chr2.fa size 92 Mbp , there was no output for a week. I want to know what went wrong

jklFF

Hi @inumanag , Just wanted to say that from my testing a small proportion of the the segdup links in bedpe output are exact duplicates. For example something like: chr1...

JHCCoder