User: mictadlo

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mictadlo0
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Posts by mictadlo

<prev • 60 results • page 1 of 6 • next >
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Filtering GFF3 file
... Hi, I have the below GFF3 file. NbV1Ch08 AUGUSTUS gene 60876 63944 0.03 + . ID=g2 NbV1Ch08 AUGUSTUS mRNA 60876 63944 0.03 + . ID=g2.t1;Note=B3 domain-containing protein Os03g0120900;Parent=g2 NbV1Ch08 AUGUSTU ...
annotation gff gff3 genome written 6 weeks ago by mictadlo0 • updated 6 weeks ago by Michael Lawrence11k
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Visualizing Orthologs and Paralogs genes
... Hi I ran [PorthoMCL](https://github.com/etabari/PorthoMCL/) and I would like to visualise the results may be as a circos plot. PorthoMCL contains two output files: - [Orthologs](https://github.com/etabari/PorthoMCL/blob/master/sample/8.all.ort.group) sample output file and - [Paralogs](https://gi ...
circos orthologs paralogs porthomcl visualizing written 5 months ago by mictadlo0 • updated 4 months ago by James W. MacDonald51k
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genetic and linkage maps construction
... Hello, We have one population consisted of 192 F3 lines resulting from a cross between two plant genomes. All our GBS reads are stored in two folders (96 files in each). 1740-44-01> ls -1 *.gz 10_S0_L001_R1_001.fastq.gz 10_S0_L001_R2_001.fastq.gz 11_S0_L001_R1_001.fastq.gz ...
snp genetic map linkage maps assembly gbs written 8 months ago by mictadlo0
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vcf to venn diagram
... Hi, I created VCF files for 5 cultivars in the following way: bcftools mpileup -Ou -f $2 ${1}/all.sorted.dedup.bam | bcftools call -mv -Ob -o ${1}/calls.bcf bcftools view -i '%QUAL>=20' ${1}/calls.bcf > ${1}/calls-gt-q20.vcf How can I create a venn-diagram out of those files? Thank you in ...
vcf snps venn diagram ggplot2 written 9 months ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... I used [HiCExplorer](https://academic.oup.com/nar/article/46/W1/W11/5036837) with help of [snakePipes](https://www.biorxiv.org/content/early/2018/09/04/407312). Do you think that HiCExplorer's output could help to get chromosome groups? ...
written 10 months ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... Our goal is to scaffold our 4000 contings into 19 scaffolds/chromosomes with help of HiC data. Similar to [this](https://www.nature.com/articles/s41438-017-0013-y/figures/1). Unfortunately, LACHESIS is not working on our cluster and therefore I am looking for alternatives. ...
written 10 months ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... Does those anchors would allow me to extract for each chromosomes a FASTA file e.g. we expecting to get 19 chromosomes so we would like to get 19 FASTA files? Do you have any code examples? ...
written 10 months ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... How is it possible to extract chromosome bins out of `ContactMatrix`? ...
written 10 months ago by mictadlo0
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from denove contig assembly to chromosome bins
... Hi, By any chance, do anyone have any recommendations which software could provide me with chromosome bins from a denovo contig assembly by using HiC data and without any annotation? Thank you in advance. ...
gothic diffhic hic hic-c hicup written 10 months ago by mictadlo0 • updated 10 months ago by Aaron Lun25k
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plot get overridden rather to overlapped
... I have the below code. Which executes twice a plot_denisities function. Unfortunately, when I execute this function again it plots a completely new picture rather overlap the two plots into one plot. #install if necessary source("http://bioconductor.org/biocLite.R") biocLite("Rsamtools" ...
rsamtools plot ggplot2 written 10 months ago by mictadlo0 • updated 10 months ago by James W. MacDonald51k

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Popular Question 9 months ago, created a question with more than 1,000 views. For Error in plot.new() : figure margins too large
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Error in plot.new() : figure margins too large

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