User: Ric

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Ric330
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Australia
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Posts by Ric

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Comment: C: bcftools for plant SNPs
... What should I set for `--ploidy` value for plants? ...
written 12 weeks ago by Ric330
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bcftools for plant SNPs
... Hi, I ran bcftools in the following way: bcftools mpileup -O b -o ${3}-${basename}.bcf -f $asm $bam bcftools call --ploidy 2 -m -o ${3}-${basename}.vcf ${3}-${basename}.bcf for a plant genome with `--ploidy 2`. However, I got this message: Note: The maximum per-sample depth with -d ...
sequence snp written 12 weeks ago by Ric330 • updated 12 weeks ago by Pierre Lindenbaum133k
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bcf: unknown file type
... Hi, I put the following SNP pipeline together: samtools faidx split-assembly/1.fa samtools mpileup -C 50 -Q 30 -f split-assembly/1.fa split-data/1.bam > BCF2-1.bcf bcftools view BCF2-1.bcf vcfutils.pl varFilter -Q 0 BCF2-1.bcf > BCF2-1-snps.vcf Unfortunately, I got ...
snp written 12 weeks ago by Ric330 • updated 12 weeks ago by Pierre Lindenbaum133k
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Comment: C: Removing a DOT after each sequence
... It turns out a DOT is also available in the middle of each sequence. How it be possible to extend the `sed` command? ...
written 12 weeks ago by Ric330
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Removing a DOT after each sequence
... Hi, I have a FASTA file which contains a `.` after each sequence. How is it possilble to remove the dot? >gene39576 gene=rps16 MVKLRLKRCGRKQRAVYRIVAIDVRSRREGKDLRKVGFYDPIKNQTYLNVPAILYFLEKG AQPTGTVQDILKKAEVFKELRPNQS. >gene39578 gene=psbK MLNTFSLIGICLNSTLFSSSFFFGKLPEAYAFLNPIV ...
sequence bioawk written 12 weeks ago by Ric330 • updated 12 weeks ago by Pierre Lindenbaum133k
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GO annotations into GFF3
... Hi, I would like to add `GO term` into the GFF3 and I found the following mapping file (`goa_uniprot_all.gpa`). gpa-version: 1.1 ! !This file contains all GO annotations for proteins in the UniProt KnowledgeBase (UniProtKB). ! !It also contains all annotations for protein comple ...
annotation go written 3 months ago by Ric330 • updated 3 months ago by JC12k
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Comment: C: Reactome Plant to Cytoscape - possible?
... How did you map your genes against Plant Reactome? ...
written 4 months ago by Ric330
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Reactome for Plants
... Hi, I downloaded the mapping files from [Plant Reactome][1]. How is it possible to map Reactome ids ==> NCBI2PlantReactome_PE_Pathway.txt <== A0A1R3FTW0 R-COL-9609608-16 A0A1R3FTW0 [cytosol] R-COL-9609573 https://plantreactome.gramene.org/PathwayBrowser/#/R-COL-9609573 Tricin biosynth ...
pathway gene annotation written 4 months ago by Ric330
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Comment: C: InterProScan for Plants
... For example, if Pathway analysis is enabled in InterProScan then it provides for Reactome a Human id `R-HSA-5689880` which can be viewed [here][1]. However, I would prefer that the software uses [Plant Reactome][2]. Is there a way to change InterProScan behaviour? [1]: https://reactome.org/Pathwa ...
written 4 months ago by Ric330
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Non redundant ID associating with GO and Pathway
... Hi, I ran Blast/diamond with our plant protein sequence against [NR][1]. In the result file I saw different types of IDs: XP_015159008.1 PHT27876.1 XP_009768969.1 XP_016509492.1 XP_016509492.1 OIT28878.1 XP_019240799.1 XP_009595915.1 OIT08863.1 XP_016514212 ...
pathway alignment go written 4 months ago by Ric330

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Student 11 weeks ago, asked a question with at least 3 up-votes. For Fastqc And Require Tools
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Scholar 5 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 5 months ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Epic Question 5 months ago, created a question with more than 10,000 views. For How to calculate the insert size for Paired-end reads
Great Question 6 months ago, created a question with more than 5,000 views. For How to calculate the insert size for Paired-end reads
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