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18 results • Page
1 of 1
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Votes
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0
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38
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 hour ago by
4fzcgueyp5
• 0
0
votes
1
reply
80
views
Annovar using R package
Annovar
gnomAD
R
updated 4 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
DKA
▴ 40
0
votes
0
replies
51
views
Finding orthologs between genome error
OMA
OMAbrowser
9 hours ago by
hemantcnaik
• 0
0
votes
0
replies
68
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 7 hours ago by
Ram
43k • written 12 hours ago by
glaciya2018
• 0
0
votes
0
replies
98
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
12 hours ago by
pramach1
▴ 40
0
votes
1
reply
95
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 11 hours ago by
Sofia
• 0 • written 15 hours ago by
mawigoj318
• 0
0
votes
0
replies
77
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
17 hours ago by
salias
• 0
0
votes
2
replies
140
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 7 hours ago by
Ram
43k • written 17 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
69
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 7 hours ago by
Ram
43k • written 17 hours ago by
newuser2024
• 0
0
votes
0
replies
60
views
Network Alignment
plugin
Cytoscape
CytoMCS
18 hours ago by
Akash D
▴ 40
0
votes
1
reply
107
views
alignment result
RNA-seq
samtools
hisat2
updated 7 hours ago by
Ram
43k • written 18 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
60
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 7 hours ago by
Ram
43k • written 20 hours ago by
Jeyong
• 0
0
votes
1
reply
113
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
195
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 7 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
0
votes
10
replies
354
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
23 hours ago by
atowns21
• 0
0
votes
5
replies
263
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
15 hours ago by
njornet
▴ 20
2
votes
4
replies
236
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
18 hours ago by
samuelkalandarov2002
▴ 10
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 17 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
18 results • Page
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Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq
by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
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