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829 results • Page
5 of 17
Sort: Votes
Rank
Views
Votes
Replies
2
votes
1
reply
273
views
ColabFold
ColabFold
updated 16 days ago by
dthorbur
★ 1.7k • written 18 days ago by
Preeti
• 0
2
votes
2
replies
270
views
Calculation variant frequencies for copy number events for a cohort
cnv
vcf
variant
frequency
19 days ago by
barslmn
★ 2.1k
2
votes
7
replies
424
views
Does vg call allow fuzzy match during SV calling?
vg
updated 22 days ago by
Jordan M Eizenga
▴ 460 • written 23 days ago by
Maxine
▴ 40
2
votes
2
replies
528
views
How to look up gene names using SNP locations on Practical Haplotype Graph
rphg
phg
12 days ago by
Dylan
• 0
2
votes
8
replies
244
views
Piping samtools to R
R
NGS
bash
samtools
22 hours ago by
joe
▴ 470
2
votes
2
replies
300
views
Choosing right GSEA background gene sets
GSEA
enrichment
analysis
updated 27 days ago by
jv
★ 1.7k • written 28 days ago by
yxwucq
• 0
2
votes
2
replies
36
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
1 hour ago by
DYLAN NICO
• 0
2
votes
1
reply
189
views
RNA-seq scaling the data for heatmap
RNA-seq
heatmap
scaling
updated 8 days ago by
matt.a.bennett25890
▴ 20 • written 8 days ago by
maplewj
▴ 10
2
votes
10
replies
558
views
Can't properly use GATK Mutect2 to call somatic variants from my tumor/normal samples pair (BAM to VCF)
vaf
gatk
vcf
genomics
mutect2
updated 15 days ago by
GenoMax
140k • written 16 days ago by
Samuel
▴ 20
2
votes
3
replies
237
views
Annotate genes from gtf file to vcf file
gtf
genomics
vcf
7 days ago by
QX
• 0
2
votes
5
replies
520
views
Weird Fragment Length distribution multiQC
Salmon
RNA-seq
paired-end
MultiQC
updated 17 days ago by
GenoMax
140k • written 27 days ago by
_deb
• 0
2
votes
3
replies
329
views
STAR alignment setting for RNA-Seq data from mouse background expressing a human ortholog
alignment
star
ortholog
rna-seq
updated 21 days ago by
swbarnes2
14k • written 22 days ago by
marionette.kent
• 0
2
votes
1
reply
242
views
Compute p-value, having log fold change
p-value
fold-change
updated 10 days ago by
Ram
43k • written 11 days ago by
Ngrin
• 0
2
votes
4
replies
379
views
How to download Accession List from NCBI on CLI?
CLI
NCBI
python
updated 23 days ago by
GenoMax
140k • written 26 days ago by
Cam
• 0
2
votes
5
replies
607
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 14 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
K
• 0
2
votes
3
replies
265
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 9 hours ago by
colindaven
6.3k • written 2 days ago by
Lissa Cruz Saavedra
• 0
2
votes
2
replies
74
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 1 hour ago by
dariober
14k • written 6 hours ago by
Pumla
• 0
2
votes
2
replies
208
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
fred.s.kremer
▴ 110
2
votes
3
replies
508
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 1 day ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
2
votes
5
replies
2.3k
views
GTF file for HIV strain pNL4-3
HIV
annotation
mapping
updated 27 days ago by
xiaoleiusc
▴ 140 • written 5.8 years ago by
caggtaagtat
★ 1.8k
2
votes
4
replies
308
views
Pearson correlation between Gene and clinical parameters
read-counts
Pearson-correlation
updated 7 days ago by
Shred
★ 1.4k • written 8 days ago by
Mary
• 0
2
votes
2
replies
332
views
Would you recommend me any tool to assign protein family membership to an aminoacidic fasta file?
protein-annotation
fasta
updated 8 days ago by
Dunois
★ 2.5k • written 7 weeks ago by
v.berriosfarias
▴ 140
2
votes
2
replies
330
views
Re. Batch effect correction in data with a design matrix without full rank
deseq2
batch
multi-factor
updated 20 days ago by
swbarnes2
14k • written 21 days ago by
JB
• 0
2
votes
4
replies
523
views
If the mane transcript isn't available should you use the canonical transcript?
ensembl
mane
gnomad
canonical
21 days ago by
amy__
▴ 160
2
votes
2
replies
229
views
Error from cgat gtf2gtf --method=genes-to-unique-chunks
RNA-Seq
GTF
cgat
27 days ago by
barrypraveen
▴ 130
2
votes
3
replies
352
views
HLA genotyping of whole genome sequencing data
HLA
genotyping
WGS
29 days ago by
Biomed-jeh
• 0
2
votes
5
replies
454
views
How do I use md5sum to check if my .fastq files from SRA Explorer have been downloaded correctly
scRNA-seq
md5
updated 26 days ago by
ATpoint
81k • written 6 weeks ago by
biotrekker
▴ 100
2
votes
2
replies
283
views
How I should set `STAR` parameters to keep all the intronic reads?
STAR
mapping
updated 28 days ago by
dsull
★ 5.7k • written 29 days ago by
Dan
▴ 180
2
votes
1
reply
219
views
ATAC-seq downstream analysis
ATAC-seq
diffbind
updated 29 days ago by
ATpoint
81k • written 29 days ago by
maplewj
▴ 10
2
votes
2
replies
262
views
compare dimplot(single cell)
DEG
scRNAseq
12 days ago by
kayah
• 0
2
votes
8
replies
436
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 8 days ago by
GenoMax
140k • written 10 days ago by
ben@f
▴ 10
2
votes
6
replies
386
views
Selection of GTF file from gencode
STAR
updated 27 days ago by
GenoMax
140k • written 27 days ago by
Nodilan
▴ 10
2
votes
2
replies
226
views
singlecell annotation
scRNA-seq
annotation
1 day ago by
kayah
• 0
2
votes
3
replies
353
views
Variant caller for Ion Torrent data
ThermoFisher
NGS
IonTorrent
Genomics
Variant-Calling
updated 18 days ago by
Brian Bushnell
20k • written 20 days ago by
adarsh_pp
▴ 40
2
votes
1
reply
171
views
Choosing an FC Threshold
statistics
rna-seq
updated 18 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
2
votes
5
replies
387
views
How to root this tree?
Phylogeny
Tree
Root
updated 28 days ago by
Michael
54k • written 29 days ago by
Mirko
• 0
2
votes
1
reply
301
views
Tool:
TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly
filtering
reads
trimming
updated 3 days ago by
Yingzi
• 0 • written 4 days ago by
Huiyang
▴ 180
2
votes
8
replies
1.2k
views
How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?
pymol
python
biopython
structural-bioinformatics
updated 22 days ago by
Wayne
★ 1.9k • written 5 weeks ago by
Aman Vishwakarma
• 0
2
votes
3
replies
246
views
Read length distribution of whole genome sequnces of human
fastq
read
fastqc
7 days ago by
Yellapu
• 0
2
votes
5
replies
451
views
Searching for gene in multiple genomes
gene
genome
alignment
sequence
updated 5 days ago by
BioinfGuru
★ 1.6k • written 6 days ago by
Miya
• 0
2
votes
6
replies
452
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
2
votes
10
replies
699
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 3 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
2
votes
2
replies
221
views
Infering the cell composition from bulk RNA-seq data for mouse
RNA-seq
deconvolution
mouse
6 days ago by
feather-W
• 0
2
votes
2
replies
181
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 2 minutes ago by
Mensur Dlakic
★ 26k • written 1 hour ago by
Ann
★ 2.4k
2
votes
1
reply
208
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 7 days ago by
Ram
43k • written 7 days ago by
Shicheng Guo
★ 9.4k
2
votes
3
replies
781
views
Inflation in Imputed data
genomic
immunochip
inflation
topmed
updated 20 days ago by
Amy
▴ 20 • written 22 months ago by
desicasares
▴ 40
2
votes
4
replies
257
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 16 days ago by
Michael
54k • written 16 days ago by
adarsh_pp
▴ 40
2
votes
5
replies
974
views
Why multiple SYMBOLS, Consequences... for Variant Effect Predictor (VEP)
VEP
updated 2 days ago by
barslmn
★ 2.1k • written 15 months ago by
gernophil
▴ 80
2
votes
2
replies
285
views
How to parallelize running vg autoindex to create graph references from VCFs with vg?
vg
27 days ago by
Ricky
▴ 10
2
votes
1
reply
273
views
DESeq and SVA for batch effect
sva
limma
batch-effect
DESeq2
updated 20 days ago by
LChart
3.9k • written 22 days ago by
michelafrancesconi9
▴ 20
829 results • Page
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Perhaps more concerning is why you have features (genes?) with small pvalue but fold-change very close to zero. It's also unusual that ther…
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Thank you for the suggestions. Unfortunately I cannot add any details for lack of information. But I will try using a different alignment a…
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They are +ve and -ve strands, but identical two by two ... I can filter that out later on. This is probably a very naive question, but what…
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Do I understand correctly that you have one gene you are interested in, but all counts are zero, right? If so, first thing could be to use …
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You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
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thank you !!
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