User: gabri

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gabri50
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Posts by gabri

<prev • 25 results • page 1 of 3 • next >
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bedtools, merge function: avoid merging intervals if separated by a single base
... Hi All, I'm using bedtools v2.26.0 to combine overlapping intervals of a bed file into “merged” intervals. I have a problem with some SNPs features (same start and end coord). These are my bed file and command line: **input.bed** chr1 70833 70833 a chr1 70837 70837 b chr1 70839 ...
bedtools merge single_base_separation written 5 months ago by gabri50 • updated 5 months ago by finswimmer11k
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Find methylated motifs in a plant genome from KineticsTool gff output
... Hi All, I successfully got the gff with the methylation information from my assembled plant genome using KineticsTool (fasta assembly + Pacbio Sequel dataset). Now I'd like to perform a downstream analysis to identify and quantify the motifs associated with these DNA modifications. As I mentioned, ...
methylation kineticstool motif pacbio plant written 8 months ago by gabri50
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Comment: C: Simple alternatives for the program Circos
... Yes I just want to show them arranged circularly. Thanks ...
written 9 months ago by gabri50
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Comment: A: Simple alternatives for the program Circos
... https://ibb.co/gDeYcz Thanks for all the suggestions. Here I put a very simple example that I manually drew to let you know what I mean. The external cirle with different colours represents the chromosomes (sequences that I don't have), the black circle inside represents the scaffolds (the sequence ...
written 9 months ago by gabri50
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Simple alternatives for the program Circos
... Dear All, I have an assembly with a certain number of scaffolds separated at chromosome level. I'd like to draw a very simple circular picture in which I can represent each chromosome with the associated scaffolds. I know that one of the most used software for these kinds of circular pictures is Ci ...
scaffolds picture circos circular chromosomes written 9 months ago by gabri50 • updated 9 months ago by Pierre Lindenbaum120k
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How to annotate LTR-retrotransposons at lineage level using LTR-digest gff output based on hmms domains
... Hi All, I have run LTR-harvest and LTR-digest on my assembly. Specifically, I have used the -hmms option of LTR-digest and the complete GyDB database of hmms for the annotation of the identified elements. Now I have a gff output. The following data are specific of a single LTR-retrotransposon. As ...
lineage ltr-retrotransposons ltr-digest written 11 months ago by gabri50 • updated 11 months ago by Biostar ♦♦ 20
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HelitronScanner running time
... Hi All, I'm running HelitronScanner on my genome assembly with the following command line: > java -jar HelitronScanner.jar scanHead -g Genome.fasta -bs 1000000 -tl > 10 -tl 10 = number of CPU -bs 1000000 = genome slice size It seems that the process is going very very slow, using less tha ...
running time helitronscanner helitron written 11 months ago by gabri50
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Training GeneMark-ES: Data format error; gmhmme3 : warning, evidence_training.gff line ignored
... Hi All, I'm trying to train GeneMark-ES for use it in a following analysis with Maker2. I'm using a sample of sequences and a gff of CDS obtained mapping some RNAseq data on these sequences with Trinity. I used Geneious to obtain the gff. This is a portion of my gff: > gff-version 3 > > ...
evidence gff genemark-es training written 11 months ago by gabri50
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Software to identify microsatellites, minisatellites and satellites in a plant genome
... Hi All, I'm annotating a bunch of long contigs from a plant genome. I'd like to identify microsatellites (2–7 bp), minisatellites (tens of bp) and satellites (hundreds of bp) whitin these contigs. I know that there are a lots of software to identify the DNA satellite. I'm thinking to try Tandem ...
genome satellite microsatellites minisatellites written 11 months ago by gabri50
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Comment: C: Remove duplicates in a Excel table summing values of associated cells
... Even this solution works really well, thank you very much! ...
written 11 months ago by gabri50

Latest awards to gabri

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver
Popular Question 8 months ago, created a question with more than 1,000 views. For Use PacBio FASTQ reads to polish\correct a PacBio Fasta assembly without Quiver

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