User: Ric

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Ric330
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Australia
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8 years, 10 months ago
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Posts by Ric

<prev • 275 results • page 2 of 28 • next >
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InterProScan for Plants
... Hi, InterProScan seems only to support Humans. Is there any similar tool for plants? Thank you in advance, ...
gene annotation protein pathways ontology written 3 months ago by Ric330
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Finding common and different genes between species
... Hi, We have two plants which one of them is the wild type. For each of them, I used the Scallop results with TransDecoder. How is possible to determine which are common and different genes between those two plants from Scallop/Transdecoder results? Thank you in advance, ...
gene annotation rna-seq written 3 months ago by Ric330
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pathway analysis in plants
... Hi, We have de-novo assembled a non-model plant genome, and we also annotated it by ourselves. Which tools are recommended to do pathway analysis? Thank you in advance, ...
gene assembly analysis annotation pathway written 3 months ago by Ric330 • updated 3 months ago by toralmanvar900
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Answer: A: annotation with Augustus
... Has been answered [here](https://github.com/Gaius-Augustus/Augustus/issues/178) ...
written 3 months ago by Ric330
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annotation with Augustus
... Hi, we have a plant genome and would like to create an annotation with Augustus. However, I am not sure about the following few parameters. - noInFrameStop=false - allow_hinted_splicesites=atac - genemodel=partial or --genemodel=complete Which settings are appropriate for a plant genome? Than ...
gene genome augustus annotation written 3 months ago by Ric330
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Failed to merge BAM files
... Hi, I have the following bash script: #!/bin/bash #usage: sh split_bam2sam-fasta_pbs.sh /path/to/reference.fasta /path/to/outputfolder/ /path/to/input/*.sorted.dedup.bam output=$2 mkdir $output merged=$(basename ${output}) echo $merged #samlist=$(printf 'I="%s" ' "$ ...
samtools bash written 4 months ago by Ric330 • updated 4 months ago by Shalu Jhanwar470
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orthomcl to venn diagram
... Hi, I found [orthomclToVenn][1] which allows to create venn diagramms from orthomcl results. Unfortunately, I do not know how to create the `families.txt` (this file details which species are in which groups, first the name of the group, then the short handles that appear in groups.txt). Example: ...
family genes ortholog venn diagram orthomcl written 5 months ago by Ric330
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Comment: C: Create de novo repeat library
... Are the below steps correct? > wget -c https://www.dfam.org/releases/Dfam_3.1/families/Dfam.embl.gz > gunzip Dfam.embl.gz > mv Dfam.embl ${CONDA_PREFIX}/share/RepeatMasker/Libraries/ > cd ${CONDA_PREFIX}/share/RepeatMasker/Libraries/ > ../util/buildRMLibFromEMBL. ...
written 7 months ago by Ric330
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Comment: C: StringTie output to train Augustus
... Thank you, is there a way or necessary to add strand information to the output of bam2hints? **UPDATE:** Bam2hints resutls: > wc -l .intron-hints.gff 438503 .intron-hints.gff . > head .intron-hints.gff NbV1Ch01 b2h intron 212732 212828 0 . . ...
written 7 months ago by Ric330
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StringTie required filtered BAM
... Hi, AUGUSTUS comes with a script which can filter BAM files filterBam –uniq –paired –pairwiseAlignment –in Aligned.out.ss.bam –out Aligned.out.ssf.bam Does StringTie does any filtering by its own or would it be possible to improve StringTie by using the above script? Thank you in advance ...
gene annotation rna-seq assembly written 8 months ago by Ric330 • updated 7 months ago by kristoffer.vittingseerup3.4k

Latest awards to Ric

Student 22 days ago, asked a question with at least 3 up-votes. For Fastqc And Require Tools
Popular Question 29 days ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Popular Question 4 weeks ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Scholar 3 months ago, created an answer that has been accepted. For A: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
Popular Question 3 months ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Epic Question 4 months ago, created a question with more than 10,000 views. For How to calculate the insert size for Paired-end reads
Great Question 4 months ago, created a question with more than 5,000 views. For How to calculate the insert size for Paired-end reads
Popular Question 4 months ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Popular Question 5 months ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Popular Question 6 months ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Popular Question 7 months ago, created a question with more than 1,000 views. For Assembly out of mapping reads to a reference genome
Popular Question 7 months ago, created a question with more than 1,000 views. For Assembly out of mapping reads to a reference genome
Popular Question 7 months ago, created a question with more than 1,000 views. For local web BLAST server
Popular Question 7 months ago, created a question with more than 1,000 views. For Assembly out of mapping reads to a reference genome
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Popular Question 12 months ago, created a question with more than 1,000 views. For circos plot to compare genomes plot
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Popular Question 14 months ago, created a question with more than 1,000 views. For circos plot to compare genomes plot
Student 15 months ago, asked a question with at least 3 up-votes. For local web BLAST server
Popular Question 16 months ago, created a question with more than 1,000 views. For Assembly out of mapping reads to a reference genome
Popular Question 16 months ago, created a question with more than 1,000 views. For Assembly out of mapping reads to a reference genome
Popular Question 18 months ago, created a question with more than 1,000 views. For Fastqc And Require Tools

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