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42 results • Page
1 of 1
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0
votes
0
replies
9
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
5 minutes ago by
analyst
▴ 30
0
votes
1
reply
18
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 10 minutes ago by
b.contreras.moreira
▴ 170 • written 48 minutes ago by
Broccoli
• 0
0
votes
0
replies
12
views
Highest variable features in single cell data
cell
single
23 minutes ago by
Kazo
• 0
0
votes
0
replies
24
views
Fetch table from clinvar database according to a list of rsid
clinvar
fetching
data
python
perl
57 minutes ago by
ashaneev07
▴ 20
0
votes
1
reply
96
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 3 hours ago by
Scooter
▴ 280 • written 22 hours ago by
Akash D
▴ 40
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 3 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
0
replies
36
views
PCA plot
DESeq2
PCAplot
4 hours ago by
Aaliya
▴ 10
0
votes
0
replies
32
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
4 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
230
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 5 hours ago by
Kevin Blighe
87k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 5 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
53
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
6 hours ago by
4fzcgueyp5
• 0
0
votes
1
reply
107
views
Annovar using R package
Annovar
gnomAD
R
updated 8 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
DKA
▴ 40
0
votes
2
replies
135
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 9 hours ago by
Mensur Dlakic
★ 27k • written 12 hours ago by
biochugs
• 0
3
votes
8
replies
375
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 2 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
0
votes
6
replies
635
views
Adding CB tag to bam file
samtools
bam
updated 11 hours ago by
swbarnes2
14k • written 6 days ago by
Maria
• 0
1
vote
10
replies
853
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
12 hours ago by
DKA
▴ 40
0
votes
0
replies
63
views
Finding orthologs between genome error
OMA
OMAbrowser
14 hours ago by
hemantcnaik
• 0
0
votes
2
replies
743
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 14 hours ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
4
replies
156
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
just now by
Bertalan_Takacs
▴ 90
0
votes
0
replies
76
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 12 hours ago by
Ram
43k • written 17 hours ago by
glaciya2018
• 0
0
votes
0
replies
66
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
17 hours ago by
David Langenberger
11k
0
votes
0
replies
127
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
17 hours ago by
pramach1
▴ 40
0
votes
14
replies
3.4k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 18 hours ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
103
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 15 hours ago by
Sofia
• 0 • written 19 hours ago by
mawigoj318
• 0
0
votes
0
replies
87
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
21 hours ago by
salias
• 0
4
votes
6
replies
290
views
To get p-values for the TPM
P-value
TPM
RSEM
57 minutes ago by
VITALA
• 0
0
votes
2
replies
150
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 12 hours ago by
Ram
43k • written 22 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
78
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 12 hours ago by
Ram
43k • written 22 hours ago by
newuser2024
• 0
1
vote
2
replies
127
views
alignment result
RNA-seq
samtools
hisat2
1 hour ago by
ahmad.sajad4541
• 0
0
votes
0
replies
74
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 12 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
70
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 12 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
2
replies
181
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
18 hours ago by
mropri
▴ 150
0
votes
2
replies
204
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 12 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
1
vote
4
replies
219
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 14 hours ago by
GenoMax
141k • written 1 day ago by
Lada
▴ 30
3
votes
13
replies
632
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 15 hours ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
0
votes
5
replies
273
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
20 hours ago by
njornet
▴ 20
3
votes
9
replies
388
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 18 hours ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
5 hours ago by
Kevin Blighe
87k
2
votes
4
replies
239
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
22 hours ago by
samuelkalandarov2002
▴ 10
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 21 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
0
votes
2
replies
562
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 4 hours ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 9 hours ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
42 results • Page
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Recent Votes
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
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)
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Recent Replies
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result
by
ahmad.sajad4541
• 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host
by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
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.…
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