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 4 weeks ago by gabri50 • updated 4 weeks ago by finswimmer9.9k
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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 4 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 5 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 5 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 5 months ago by gabri50 • updated 5 months ago by Pierre Lindenbaum116k
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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 7 months ago by gabri50 • updated 7 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 7 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 7 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 7 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 7 months ago by gabri50

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Popular Question 4 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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