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43 results • Page
1 of 1
Sort: Views
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Views
Votes
Replies
2
votes
6
replies
6.9k
views
Extracting chimeric reads from mapping
RNA-Seq
alignment
samtools
bwa
updated 22 hours ago by
doggie
• 0 • written 6.2 years ago by
Anushka
▴ 20
3
votes
2
replies
953
views
How do I download a list of genes involved in cellular metabolism (in humans) based on a Reactome pathway?
genes
metabolism
GO
Reactome
updated 21 hours ago by
el24
▴ 40 • written 2.0 years ago by
emmah
• 0
2
votes
9
replies
637
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
16 hours ago by
ian.will
▴ 10
8
votes
7
replies
515
views
How to filter .fasta file based on conditional statement
abundance
filtering
fasta
vsearch
5 hours ago by
rob_DNA
▴ 20
5
votes
5
replies
383
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 21 hours ago by
i.sudbery
18k • written 1 day ago by
sehriban.buyukkilic
• 0
0
votes
6
replies
345
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
20 hours ago by
tw_140
• 0
0
votes
1
reply
337
views
How to use conumee segment mean for gistic input
genomics
gistic
NGS
methylation
conumee
updated 23 hours ago by
sativus
▴ 10 • written 14 months ago by
Thind amarinder
▴ 340
0
votes
9
replies
332
views
Where is the index command?
samtools
updated 1 hour ago by
Michael
53k • written 18 hours ago by
luque007
• 0
4
votes
6
replies
334
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
17 hours ago by
cee28
▴ 30
3
votes
6
replies
328
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 21 hours ago by
NextGenSeek
• 0 • written 1 day ago by
singhankit973
• 0
0
votes
4
replies
275
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
16 hours ago by
DINESHR
• 0
0
votes
5
replies
248
views
HTseq reports missing attribute name
htseq
updated 15 minutes ago by
Istvan Albert
99k • written 2 days ago by
Bjorn
• 0
0
votes
3
replies
242
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
15 hours ago by
cook.675
▴ 200
0
votes
1
reply
208
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 13 hours ago by
Ram
41k • written 6 days ago by
bioinfo
▴ 60
3
votes
2
replies
208
views
Mapping quality in `vg giraffe`
vg
3 hours ago by
Wenhai
• 0
0
votes
4
replies
200
views
Making multiple box plots with relative abundance in R
R
Boxplots
22 hours ago by
ohtang7
▴ 40
2
votes
3
replies
183
views
Blastn DB issue
cgmlst
blastn
updated 10 hours ago by
Philipp Bayer
8.1k • written 1 day ago by
hakhasan
• 0
1
vote
1
reply
179
views
Match variants for allele frequency, LD score, and other features
snp
22 hours ago by
Jautis
▴ 520
1
vote
2
replies
175
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
7 hours ago by
eamaunders
• 0
3
votes
3
replies
166
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 12 hours ago by
Jeremy
▴ 840 • written 22 hours ago by
ohtang7
▴ 40
2
votes
2
replies
155
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
ATpoint
78k • written 17 hours ago by
newbee
▴ 40
0
votes
2
replies
155
views
What type of cancer did they study in this paper?
cancer
RNAseq
single-cell
updated 21 hours ago by
GenoMax
136k • written 21 hours ago by
JACKY
▴ 120
0
votes
3
replies
144
views
ERROR FILE EXTENSION
Prokka
7 hours ago by
syirah4
• 0
0
votes
2
replies
141
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 3 hours ago by
fracarb8
★ 1.3k • written 16 hours ago by
synat.keam
▴ 80
0
votes
0
replies
128
views
Mapping Mouse RNAseq Marker Genes to Reactome Pathways
single-cell
pathways
reactome
RNAseq
gene
20 hours ago by
el24
▴ 40
0
votes
3
replies
120
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
4 hours ago by
J
• 0
1
vote
3
replies
113
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 2 hours ago by
Basti
★ 1.8k • written 6 hours ago by
CTLong
▴ 20
0
votes
4
replies
111
views
Can you help me to download list of miRNA from a SRA under a bioproject ?
bioproject
mirna
updated 37 minutes ago by
ATpoint
78k • written 4 hours ago by
abourrieau
• 0
0
votes
1
reply
107
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
updated 8 hours ago by
Tao
▴ 30 • written 18 hours ago by
Bryan
▴ 10
0
votes
1
reply
107
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 3 hours ago by
Nitin Narwade
★ 1.5k • written 19 hours ago by
tss243
• 0
0
votes
1
reply
91
views
R script in docker
R
Visual_studio_code
Docker
5 hours ago by
mrashad
▴ 70
0
votes
0
replies
89
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
26 minutes ago by
aheinzel
▴ 130
0
votes
0
replies
82
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 23 hours ago by
GenoMax
136k • written 23 hours ago by
PierreGT
• 0
0
votes
0
replies
79
views
deeptools k-means clustering
heatmap
deeptools
chipseq
18 hours ago by
biology_inform
▴ 50
0
votes
0
replies
71
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 22 hours ago by
GenoMax
136k • written 23 hours ago by
sativus
▴ 10
0
votes
0
replies
68
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
16 hours ago by
luckyday1661
• 0
0
votes
0
replies
61
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
16 hours ago by
DINESHR
• 0
1
vote
3
replies
56
views
Tools or R / Python packages to perfom ML models
Python
machine-learning
R
transcriptomics
updated 3 minutes ago by
Michael
53k • written 2 hours ago by
sil_bioinfo
▴ 30
0
votes
1
reply
55
views
Salmon indices differences
salmon
RNAseq
index
refgenie
decoy
updated 2 hours ago by
ATpoint
78k • written 3 hours ago by
enee
▴ 10
0
votes
0
replies
42
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
5 hours ago by
hellokwmin
• 0
0
votes
0
replies
37
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
6 hours ago by
maxlaubstein
• 0
0
votes
0
replies
31
views
PAML Troubleshooting Help
PAML
codeml
4 hours ago by
sebabiokr
▴ 10
0
votes
1
reply
19
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 7 minutes ago by
Istvan Albert
99k • written 1 hour ago by
Jingfang
• 0
43 results • Page
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Comment: Tools or R / Python packages to perfom ML models
Comment: How can I amend the output of a DIAMOND python script?
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
A: How to add biological annotations using R
Answer: Mapping quality in `vg giraffe`
Answer: Mapping quality in `vg giraffe`
Answer: Comparing 3 Data Sets using DeSeq and Heatmaps
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Recent Replies
Answer: Tools or R / Python packages to perfom ML models
by
Michael
53k
How about TensorFlow? https://www.tensorflow.org/overview You can run the examples directly in Colab. This short introduction uses Ke…
Comment: In what case there are RR reads but no LL reads when detect inversions using IGV
by
Istvan Albert
99k
you should visualize the image as pairs (view-as-pairs) the image you show is not quite right, it is also important to note what gets color…
Comment: Tools or R / Python packages to perfom ML models
by
sil_bioinfo
▴ 30
Hi, I'm more comfortable with R right now. I found the R package "mlr3", I don't know if you know of any others. I would appreciate it if y…
Comment: HTseq reports missing attribute name
by
Istvan Albert
99k
sounds like your genome file is not quite correct, you need to make sure it is in FASTA format all the way through, perhaps get it from a r…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ?
by
ATpoint
78k
I it was available then you would see entries there. Still, be aware that this is raw sequencing data, so it's not just a list of miRNAs. C…
Comment: Tools or R / Python packages to perfom ML models
by
rpolicastro
12k
R and Python have access to most ML methods, it's just a matter of learning either of the languages and then finding which libraries are po…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
ATpoint
78k
Seconding that. Is there anything else that you can use for QC, like some Trypan Blue stain of the cells right before loading the chip? Is …
Comment: Where is the index command?
by
Michael
53k
samtools index (like genral programs you install on your machine) should run without sudo, if it doesn't, you might want to check the acces…
Comment: Where is the index command?
by
Michael
53k
I didn't know you were using WSL. Possibly the damage you can do with that is limited to the WSL environment and the worst thing that can h…
Comment: Is bisulfite-seq data from different studies comparable with each other?
by
Basti
★ 1.8k
There is no general rule, what you can apply depends on the nature of each dataset you intend to integrate (tissue, condition, technique, s…
Comment: Where is the index command?
by
Michael
53k
Running this is always a good idea.
Answer: Salmon indices differences
by
ATpoint
78k
In theory the full genome decoy is the best since it includes the entire genome, hence decoying potential spurious mappings due to DNA cont…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ?
by
Nitin Narwade
★ 1.5k
You can directly ask authors but as it is still on bioRxiv I don't think they can share this data with you until it get published somewhere…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ?
by
abourrieau
• 0
Thank you, I had thought about this possibility but I don't see where it is indicated on the NCBI website: : https://www.ncbi.nlm.nih.gov/b…
Comment: Cellcyclescoring did not work in Seurat V5
by
fracarb8
★ 1.3k
You can try to merge the layer together with `data.filt <- JoinLayers(data.filt)`
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