User: Ric
Ric • 330
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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
Ric • 330
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... 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 ...
written 12 weeks ago by
Ric • 330
• updated
12 weeks ago by
Pierre Lindenbaum ♦ 133k
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... 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 ...
written 12 weeks ago by
Ric • 330
• updated
12 weeks ago by
Pierre Lindenbaum ♦ 133k
0
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1
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... 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
Ric • 330
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... 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 ...
written 12 weeks ago by
Ric • 330
• updated
12 weeks ago by
Pierre Lindenbaum ♦ 133k
0
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1
answer
153
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1
answer
... 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 ...
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... How did you map your genes against Plant Reactome? ...
written 4 months ago by
Ric • 330
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... 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 ...
written 4 months ago by
Ric • 330
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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
Ric • 330
0
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... 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 ...
written 4 months ago by
Ric • 330
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