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46 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
1
view
How to find node Postion and source(sample) ?
vg
just now by
zhang yi xing
▴ 20
0
votes
2
replies
77
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
ChIP-seq
DiffBind
4 minutes ago by
DINESHR
• 0
0
votes
0
replies
4
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
10 minutes ago by
Richard Fontaine
• 0
0
votes
0
replies
11
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
55 minutes ago by
cee28
• 0
0
votes
1
reply
42
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 1 hour ago by
rpolicastro
12k • written 2 hours ago by
O.rka
▴ 710
0
votes
2
replies
82
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 2 hours ago by
cmdcolin
★ 3.4k • written 3 hours ago by
Dylan C-C
• 0
1
vote
3
replies
102
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 1 hour ago by
dsull
★ 5.0k • written 4 hours ago by
RNAseqer
▴ 250
1
vote
5
replies
167
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 3 hours ago by
ATpoint
78k • written 6 hours ago by
singhankit973
• 0
0
votes
1
reply
72
views
bam or VCF files from GSE75010
bam
file
or
VCF
updated 6 hours ago by
ATpoint
78k • written 6 hours ago by
ahonya
• 0
0
votes
0
replies
79
views
Bcftools consensus when reference is a deletion
consensus
vcf
6 hours ago by
selplat21
▴ 20
0
votes
1
reply
115
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 7 hours ago by
singh.vijender
▴ 80 • written 16 hours ago by
DareDevil
★ 3.3k
0
votes
4
replies
206
views
How to deeply sequence long inserts
NGS
phage
read
display
Long
updated 6 hours ago by
Brian Bushnell
19k • written 12 hours ago by
Ryan
• 0
0
votes
1
reply
80
views
VCF conservation into Treemix
Treemix
Plink
VCF
updated 7 hours ago by
singh.vijender
▴ 80 • written 8 hours ago by
reza
▴ 300
0
votes
2
replies
139
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
6 hours ago by
harter-ainsworth.izaak
• 0
0
votes
0
replies
51
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
9 hours ago by
rbronste
▴ 420
0
votes
2
replies
133
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 4 hours ago by
dsull
★ 5.0k • written 11 hours ago by
sehriban.buyukkilic
• 0
3
votes
2
replies
129
views
Moving AF tag to new column in a VCF file
mutect2
vcf
6 hours ago by
Christian
▴ 30
1
vote
4
replies
205
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
updated 10 hours ago by
GenoMax
136k • written 23 hours ago by
Jimmy
▴ 10
0
votes
1
reply
107
views
The difference blastn output when using subject and db options
genome
blastn
mite
annotation
tracker
updated 14 hours ago by
GenoMax
136k • written 17 hours ago by
praasu
▴ 40
1
vote
3
replies
192
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 8 hours ago by
Nitin Narwade
★ 1.5k • written 15 hours ago by
Bine
▴ 50
1
vote
3
replies
176
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts
HISAT2
RNA-seq
updated 14 hours ago by
GenoMax
136k • written 16 hours ago by
Hamtaro
▴ 10
0
votes
1
reply
103
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 14 hours ago by
barslmn
★ 2.0k • written 16 hours ago by
Saurabh
• 0
0
votes
2
replies
119
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
1 minute ago by
GeneBC12
• 0
1
vote
1
reply
119
views
Mapping quality in `vg giraffe`
vg
updated 17 hours ago by
Xian
▴ 40 • written 22 hours ago by
Wenhai
• 0
2
votes
1
reply
110
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 14 hours ago by
barslmn
★ 2.0k • written 18 hours ago by
jiyoung
▴ 20
2
votes
4
replies
393
views
Protein Database
protein
course
database
updated 18 hours ago by
Elisabeth Gasteiger
★ 2.3k • written 4 days ago by
Mery
• 0
0
votes
0
replies
61
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
19 hours ago by
Smriti
▴ 10
0
votes
6
replies
233
views
I made an error when using metawrap to binning
metagenome
binning
metawrap
19 hours ago by
alice005201314
• 0
1
vote
4
replies
210
views
Bowtie mapping for single_end read
bowtie
9 hours ago by
Rita
• 0
0
votes
0
replies
62
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
20 hours ago by
cook.675
▴ 200
0
votes
4
replies
138
views
MRI VBM issue
MRI
VBM
ROI
Rhesus
21 hours ago by
Ethan Lee
• 0
5
votes
3
replies
192
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
updated 8 hours ago by
Brian Bushnell
19k • written 1 day ago by
jiyoung
▴ 20
0
votes
4
replies
217
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
9 hours ago by
tw_140
• 0
1
vote
2
replies
210
views
Best practices for unstranded sequences in featureCounts
featurecounts
overlapping
unstranded
18 hours ago by
Enrique
• 0
9
votes
16
replies
662
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
4 hours ago by
analyst
▴ 10
0
votes
3
replies
210
views
merged rs number information
merged
dbsnp
23 hours ago by
sskimvd
• 0
2
votes
1
reply
221
views
EnhancedVolcano underrepresenting DEGs
R
updated 13 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
2
votes
4
replies
338
views
Human mitochondrial reference genome
reference
genome
mitochondria
6 hours ago by
singhankit973
• 0
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
19 hours ago by
je71xusa
• 0
4
votes
9
replies
563
views
Working with NCBI downloadable Datasets
NCBI
Genedata
Datasets
updated 21 hours ago by
rfran010
▴ 880 • written 6 days ago by
jakob.olsson04
• 0
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 7 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
1
vote
6
replies
457
views
frequency plot for peaks
chip-seq
chipseeker
updated 1 hour ago by
Ankit
▴ 400 • written 15 days ago by
Mehwish
▴ 10
3
votes
5
replies
488
views
Circular genome browser
genome-browser
circular-genome
updated 12 hours ago by
cmdcolin
★ 3.4k • written 27 days ago by
giammafer
▴ 20
3
votes
2
replies
627
views
CPTAC data, download, merge
CPTAC
merging
seq
data
RNA
updated 16 hours ago by
Mohita
▴ 50 • written 16 months ago by
Rob
▴ 160
7
votes
11
replies
1.7k
views
Technical replicates in Microarray data
GEO
Microarray
updated 21 hours ago by
cwwong13
▴ 20 • written 22 months ago by
Fatemeh Nabizadeh
▴ 10
4
votes
4
replies
1.9k
views
How to do simple pathway analysis?
rna-seq
genome
gene
updated 10 hours ago by
he1k
• 0 • written 4.5 years ago by
Seq225
▴ 110
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Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
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Comment: unicycler error : [Errno 13] Permission denied:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
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Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GeneBC12
• 0
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
• 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
dsull
★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM?
by
rpolicastro
12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks
by
Ankit
▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
cmdcolin
★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
rpolicastro
12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file
by
ATpoint
78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
ATpoint
78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods
by
dsull
★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
RNAseqer
▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
Nitin Narwade
★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file
by
Enrique
• 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file
by
ATpoint
78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
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