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248 results • Page
3 of 5
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
69
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
3
votes
5
replies
240
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 2 days ago by
GenoMax
141k • written 3 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
84
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
3
votes
5
replies
530
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
2 days ago by
n_navy
• 0
0
votes
0
replies
70
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
2 days ago by
sativus
▴ 20
6
votes
3
replies
163
views
Interpretting IGV output
IGV
updated 2 days ago by
Carlo Yague
8.7k • written 3 days ago by
analyst
▴ 30
0
votes
1
reply
169
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
Ayush
• 0
0
votes
0
replies
76
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
2 days ago by
Biostars2200
• 0
1
vote
5
replies
298
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
1 day ago by
anasjamshed
▴ 120
0
votes
0
replies
121
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by
Carlo Yague
8.7k • written 3 days ago by
Atul K.
• 0
3
votes
2
replies
261
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
2 days ago by
kristiewyleung
• 0
2
votes
5
replies
428
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
0
votes
0
replies
136
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 3 days ago by
Ram
43k • written 4 days ago by
sainavyav22
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
4 days ago by
rthapa
▴ 90
0
votes
0
replies
131
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
4 days ago by
Mamatha Y S
• 0
0
votes
0
replies
127
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 3 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
513
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 4 days ago by
ATpoint
82k • written 5 days ago by
rheab1230
▴ 140
0
votes
2
replies
252
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
7
votes
6
replies
450
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
3 days ago by
analyst
▴ 30
1
vote
1
reply
253
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Bioinformatician
• 0
1
vote
0
replies
536
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
4 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
293
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 5 days ago by
Ram
43k • written 5 days ago by
Nina
• 0
2
votes
5
replies
508
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 4 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Giorgio
• 0
2
votes
1
reply
281
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 5 days ago by
GenoMax
141k • written 5 days ago by
rebecca.calvo
• 0
0
votes
0
replies
209
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
4 days ago by
abhishekghadge
• 0
2
votes
5
replies
676
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
0
votes
0
replies
184
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 5 days ago by
Ram
43k • written 5 days ago by
mja
• 0
0
votes
0
replies
186
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
5 days ago by
Nitin
• 0
1
vote
5
replies
550
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 5 days ago by
GenoMax
141k • written 5 days ago by
Luka
• 0
0
votes
0
replies
186
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by
Ram
43k • written 5 days ago by
yifangt86
▴ 60
0
votes
0
replies
179
views
Chemical structure validation
structure
cap
validation
metabolite
5 days ago by
Rodolfo Adrián
• 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 4 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 5 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
0
votes
0
replies
202
views
Copy number variation plot
Copy-number-variation
genomics
updated 5 days ago by
Ram
43k • written 5 days ago by
Emmi
• 0
1
vote
5
replies
687
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 5 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
rrehimi
• 0
0
votes
0
replies
175
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
5 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
279
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by
Ram
43k • written 5 days ago by
Kazo
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 5 days ago by
ATpoint
82k • written 7.1 years ago by
boymin2020
▴ 80
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 4 days ago by
ATpoint
82k • written 5 days ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
409
views
Plink merge errors.
cygwin64
bed
PLINK
5 days ago by
Dinmukhamed
• 0
0
votes
0
replies
193
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 5 days ago by
Ram
43k • written 5 days ago by
Dinmukhamed
• 0
0
votes
0
replies
192
views
miRDeep2: How to get the read counts
mirdeep2
5 days ago by
Atul K.
• 0
3
votes
4
replies
645
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
2 days ago by
rahu
• 0
0
votes
0
replies
199
views
Lncipedia GTF file error
Proteomics
updated 5 days ago by
Ram
43k • written 5 days ago by
atharvakarkare14
▴ 10
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 5 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
462
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 4 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
0
votes
2
replies
531
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
11
votes
12
replies
933
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 6 days ago by
Ram
43k • written 6 days ago by
iamsmor
• 0
0
votes
0
replies
212
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
N.Y.Wiyana-Hewage
• 0
248 results • Page
3 of 5
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
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.…
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.
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