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690 results • Page
4 of 14
Sort: replies
Rank
Views
Votes
Replies
1
vote
4
replies
454
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
21 days ago by
hagl
▴ 10
0
votes
4
replies
410
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
8 days ago by
beginner123
• 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 9 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
0
votes
4
replies
319
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
1 day ago by
Bibi
• 0
3
votes
4
replies
353
views
Truncated metadata file report from ENA Portal API
ena
python
10 days ago by
Giulia
• 0
5
votes
4
replies
740
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
27 days ago by
kirillkirilenko
▴ 40
1
vote
4
replies
301
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
5 days ago by
Arton
▴ 10
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 26 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
1
vote
4
replies
421
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
13 days ago by
heelpPlease
• 0
0
votes
4
replies
431
views
Highest variable features in single cell data
single-cell
13 days ago by
carolofharvest
▴ 40
3
votes
4
replies
491
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 14 days ago by
Gordon Smyth
★ 7.2k • written 17 days ago by
SHN
▴ 40
2
votes
4
replies
2.5k
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 26 days ago by
ZhangYuanfeng
• 0 • written 2.5 years ago by
Frazier Baker
• 0
1
vote
4
replies
346
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 2 days ago by
Joe
21k • written 12 days ago by
cput
• 0
1
vote
4
replies
502
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 27 days ago by
atowns21
• 0 • written 6 months ago by
ara
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 7 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
4
replies
302
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 15 hours ago by
dthorbur
★ 2.0k • written 3 days ago by
Umer
▴ 50
0
votes
4
replies
346
views
Merge clusters in Seurat UMAP
seurat
umap
4 days ago by
kilcdincer
▴ 10
6
votes
4
replies
454
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
18 days ago by
Estevão
▴ 10
0
votes
4
replies
354
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 21 days ago by
Ram
43k • written 21 days ago by
Hamtaro
▴ 50
2
votes
4
replies
2.8k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 21 days ago by
Medhat
9.7k • written 2.0 years ago by
Vitor1
▴ 120
2
votes
4
replies
241
views
Help with IGV abbreviation
igv
updated 6 days ago by
Ram
43k • written 7 days ago by
GeneC
• 0
2
votes
4
replies
314
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
6 days ago by
Esraa
• 0
2
votes
4
replies
390
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
27 days ago by
samuelkalandarov2002
▴ 10
0
votes
4
replies
229
views
GO analysis: p-value range
GO
R
updated 22 hours ago by
Matthias Zepper
4.6k • written 1 day ago by
sooni
▴ 20
0
votes
4
replies
333
views
Correlation Analysis
statistics
methylation
NGS
expression
10 days ago by
Researcher
▴ 30
3
votes
4
replies
426
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
25 days ago by
QX
• 0
3
votes
4
replies
422
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Pierre Lindenbaum
161k
0
votes
4
replies
322
views
Genbank File Format
gbkformat
21 days ago by
alenew.am
• 0
6
votes
4
replies
362
views
Details on salmon index
Salmon
updated 3 days ago by
Rob
6.6k • written 4 days ago by
Lorenzo
• 0
1
vote
4
replies
524
views
cellranger error message
multiplexing
cellranger
updated 10 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
2
votes
4
replies
406
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 27 days ago by
swbarnes2
14k • written 28 days ago by
dxj294
• 0
2
votes
4
replies
282
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 5 days ago by
yura.grabovska
▴ 90 • written 5 days ago by
ev97
▴ 20
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 7 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
1
vote
4
replies
431
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 10 days ago by
GenoMax
142k • written 4 weeks ago by
aniigodwinn
• 0
3
votes
4
replies
345
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 3 days ago by
Jeremy Leipzig
22k • written 5 days ago by
Ali
• 0
0
votes
4
replies
272
views
Galaxy StringTie error
stringtie
galaxy
6 days ago by
trkfs
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 6 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
1
vote
4
replies
300
views
Add stats to boxplot in R
stats
R
5 days ago by
Ghada
• 0
2
votes
4
replies
351
views
from row count to tpm
tpm
row-count
normalization
updated 20 days ago by
Ram
43k • written 28 days ago by
michelafrancesconi9
▴ 20
1
vote
4
replies
362
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 6 days ago by
Juke34
8.6k • written 7 days ago by
Vijith
▴ 30
0
votes
4
replies
353
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 2 days ago by
txema.heredia
▴ 130 • written 4 days ago by
Ngrin
• 0
1
vote
4
replies
237
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 12 hours ago by
Ram
43k • written 14 hours ago by
Harshita
• 0
2
votes
4
replies
182
views
Filter Genome for Specific Sites
bedtools
updated 12 hours ago by
Ram
43k • written 14 hours ago by
Anita
• 0
1
vote
4
replies
415
views
Segmentation error while using a tool
smalt
updated 16 days ago by
Mensur Dlakic
★ 27k • written 17 days ago by
Ruqaiya
• 0
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
18 days ago by
eebloom
▴ 80
0
votes
4
replies
250
views
Sequencing Depth (Read Depth) Calculations
depth
5 days ago by
LucisTheFather
• 0
3
votes
4
replies
766
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
28 days ago by
rahu
• 0
2
votes
4
replies
724
views
Count all variants from vcf file
variants
vcf
Count
updated 13 days ago by
Pierre Lindenbaum
161k • written 21 months ago by
t.ali
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 12 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
2
votes
4
replies
297
views
Where to get the following bed file?
WES
bed
reference
file
updated 14 days ago by
GenoMax
142k • written 14 days ago by
wyuan37
• 0
690 results • Page
4 of 14
Recent Votes
A: Where to find PCR duplicate reads in bam file?
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
A: Bcftools merge taking too much time and producing large file
Answer: Kraken2 database
A: Why gene expression data should be log2 transformed?
Answer: Filter Genome for Specific Sites
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marco.barr
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▴ 200
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★ 4.3k
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Recent Replies
Comment: Add stats to the plot
by
marco.barr
▴ 130
if don't work try binding the stats without group. stat_data4 <- data4.ts %>% ungroup() %>% t.test(data = ., value ~ Cond…
Comment: Nextflow docker: Error response from daemon
by
Pierre Lindenbaum
161k
you should ask : https://github.com/nf-core/sarek/issues/
Comment: Where to find old version of GATK best practice
by
Pierre Lindenbaum
161k
https://github.com/gatk-workflows ?
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
Hi, if you can please post a separate question with inputs and expected output, reply here with a link to it, and I'll take a look.
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi again Alex, sorry to ask another question about this, but how can I tweak this code to keep **all** of the SNPs that pass the threshold …
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Hello I have a quick question, I did as you said , and further added the traits, found the correlation among the modules and the traits us…
Comment: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
ojaswinipandey
• 0
Thank you so much Dave.
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
Dave Carlson
★ 1.7k
The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi Mohamed, I also thought the same thing but we run the risk of inserting other errors perhaps by modifying the function. I tried but I ha…
Comment: Trimming tool
by
Ram
43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
This post does not fit the theme of this forum.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
Hi, Congratulations but this is not LinkedIn, we are not a place to showcase your professional accomplishments. This does not fall under t…
Comment: Kraken2 Custom Database non-deterministic results
by
GenoMax
142k
Many (most?) programs related to NGS data analysis produce non-deterministic output (unless they explicitly offer an option to produce dete…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
• 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
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