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113,842 results • Page
1 of 2277
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0
votes
0
replies
12
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
50 minutes ago by
luckyday1661
• 0
0
votes
1
reply
13
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 4 minutes ago by
bk11
★ 1.8k • written 55 minutes ago by
synat.keam
▴ 80
0
votes
0
replies
11
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
1 hour ago by
DINESHR
• 0
0
votes
1
reply
32
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 1 hour ago by
rpolicastro
12k • written 2 hours ago by
newbee
▴ 40
0
votes
1
reply
70
views
Where is the index command?
index
command
updated 2 hours ago by
Michael
53k • written 2 hours ago by
luque007
• 0
0
votes
0
replies
39
views
deeptools k-means clustering
heatmap
deeptools
chipseq
2 hours ago by
biology_inform
▴ 50
0
votes
0
replies
31
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
3 hours ago by
Bryan
▴ 10
0
votes
0
replies
34
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
4 hours ago by
tss243
• 0
772
votes
164
replies
128k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
3
votes
6
replies
285
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 5 hours ago by
NextGenSeek
• 0 • written 1 day ago by
singhankit973
• 0
0
votes
2
replies
103
views
What type of cancer did they study in this paper?
cancer
RNAseq
single-cell
updated 6 hours ago by
GenoMax
136k • written 6 hours ago by
JACKY
▴ 120
0
votes
0
replies
51
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
6 hours ago by
aheinzel
▴ 130
1
vote
2
replies
91
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 6 hours ago by
ATpoint
78k • written 7 hours ago by
ohtang7
▴ 30
0
votes
0
replies
43
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 6 hours ago by
GenoMax
136k • written 7 hours ago by
sativus
▴ 10
0
votes
0
replies
53
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 8 hours ago by
GenoMax
136k • written 8 hours ago by
PierreGT
• 0
5
votes
5
replies
337
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 6 hours ago by
i.sudbery
18k • written 1 day ago by
sehriban.buyukkilic
• 0
0
votes
0
replies
54
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
8 hours ago by
reaset41
• 0
0
votes
4
replies
162
views
Making multiple box plots with relative abundance in R
R
Boxplots
7 hours ago by
ohtang7
▴ 30
1
vote
1
reply
103
views
Two identical reads in my bam files but with a different in CIGAR are mapped in a different location in IGV
pysam
9 hours ago by
ManuelDB
▴ 80
0
votes
0
replies
44
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
9 hours ago by
jorge.cortes.miranda
• 0
4
votes
7
replies
205
views
regarding blast result interpretation
blast
updated 8 hours ago by
dthorbur
▴ 870 • written 10 hours ago by
Raman
• 0
2
votes
2
replies
122
views
Blastn DB issue
cgmlst
blastn
10 hours ago by
hakhasan
• 0
0
votes
1
reply
109
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
updated 9 hours ago by
Nitin Narwade
★ 1.5k • written 11 hours ago by
eamaunders
• 0
1
vote
2
replies
152
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 13 hours ago by
DBScan
▴ 210 • written 17 hours ago by
applepie
• 0
0
votes
1
reply
306
views
FVA on Sybil
R
Sybil
metabolic
fba
fva
updated 14 hours ago by
Thomas
• 0 • written 22 months ago by
isM15
• 0
0
votes
3
replies
180
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
just now by
cook.675
▴ 200
0
votes
1
reply
120
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 10 hours ago by
rpolicastro
12k • written 18 hours ago by
saipra003
▴ 10
0
votes
0
replies
77
views
How to find node Postion and source(sample) ?
vg
19 hours ago by
zhang yi xing
▴ 20
0
votes
4
replies
216
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
1 hour ago by
DINESHR
• 0
0
votes
0
replies
72
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
19 hours ago by
Richard Fontaine
• 0
4
votes
6
replies
258
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
2 hours ago by
cee28
▴ 30
1
vote
1
reply
133
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 9 hours ago by
rpolicastro
12k • written 21 hours ago by
O.rka
▴ 710
0
votes
2
replies
310
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 22 hours ago by
cmdcolin
★ 3.4k • written 22 hours ago by
Dylan C-C
• 0
3
votes
4
replies
251
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 13 hours ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
RNAseqer
▴ 250
0
votes
1
reply
122
views
bam or VCF files from GSE75010
bam
file
or
VCF
updated 1 day ago by
ATpoint
78k • written 1 day ago by
ahonya
• 0
0
votes
0
replies
113
views
Bcftools consensus when reference is a deletion
consensus
vcf
1 day ago by
selplat21
▴ 20
1
vote
1
reply
163
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 1 day ago by
singh.vijender
▴ 100 • written 1 day ago by
DareDevil
★ 3.3k
0
votes
5
replies
288
views
How to deeply sequence long inserts
NGS
phage
read
display
Long
updated 13 hours ago by
GenoMax
136k • written 1 day ago by
Ryan
• 0
0
votes
1
reply
113
views
VCF conservation into Treemix
Treemix
Plink
VCF
updated 1 day ago by
singh.vijender
▴ 100 • written 1 day ago by
reza
▴ 300
0
votes
2
replies
182
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
1 day ago by
harter-ainsworth.izaak
• 0
0
votes
0
replies
81
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
1 day ago by
rbronste
▴ 420
3
votes
2
replies
163
views
Moving AF tag to new column in a VCF file
mutect2
vcf
1 day ago by
Christian
▴ 30
1
vote
4
replies
238
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Jimmy
▴ 10
0
votes
1
reply
135
views
The difference blastn output when using subject and db options
genome
blastn
mite
annotation
tracker
updated 1 day ago by
GenoMax
136k • written 1 day ago by
praasu
▴ 40
1
vote
3
replies
226
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 1 day ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
Bine
▴ 50
1
vote
7
replies
327
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts
HISAT2
RNA-seq
12 hours ago by
Hamtaro
▴ 10
0
votes
1
reply
135
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 1 day ago by
barslmn
★ 2.0k • written 1 day ago by
Saurabh
• 0
1
vote
6
replies
304
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
17 hours ago by
CTLong
▴ 10
1
vote
1
reply
151
views
Mapping quality in `vg giraffe`
vg
updated 1 day ago by
Xian
▴ 40 • written 1 day ago by
Wenhai
• 0
2
votes
1
reply
141
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 1 day ago by
barslmn
★ 2.0k • written 1 day ago by
jiyoung
▴ 20
113,842 results • Page
1 of 2277
Recent Votes
Comment: Merging several vcf files for GWAS?
Comment: p-value combination methods
Comment: bwa mem hangs after a few thousand reads
Comment: bwa mem hangs after a few thousand reads
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
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Comment: Viral genes not showing up in combined mouse+virus alignment
by
cook.675
▴ 200
I figured it out! The GTF.featureType uses 'exon' by default which is present in the mouse GTF but the viral GTF file has no exon feature n…
Comment: Cellcyclescoring did not work in Seurat V5
by
bk11
★ 1.8k
This vignette will help you. [https://satijalab.org/seurat/articles/seurat5_cell_cycle_vignette][1] [1]: https://satijalab.org/seurat/…
Comment: Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
by
ian.will
▴ 10
Yep gave that a go and proceeding with the analysis. Thanks again.
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
• 0
Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using …
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
rpolicastro
12k
Assuming Cell Ranger was ran correctly it's unlikely that the sample is useable. It looks like most droplets were probably empty.
Comment: bwa mem hangs after a few thousand reads
by
cee28
▴ 30
Here is the output with the "-v 4" flag (not showing all the @SQ comments) : > @SQ SN:chrUn_GL000214v1 LN:137718 @SQ SN:chrUn_KI270742v1 L…
Answer: Where is the index command?
by
Michael
53k
There is a ready-made package for samtools, simply do apt install samtools Also, your screenshot shows you are using the root account…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 180
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 180
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Comment: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
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