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42 results • Page
1 of 1
Sort: replies
Rank
Views
Votes
Replies
9
votes
16
replies
677
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
11 hours ago by
analyst
▴ 10
1
vote
6
replies
489
views
frequency plot for peaks
chip-seq
chipseeker
updated 8 hours ago by
Ankit
▴ 400 • written 15 days ago by
Mehwish
▴ 10
1
vote
6
replies
213
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts
HISAT2
RNA-seq
updated 30 minutes ago by
GenoMax
136k • written 23 hours ago by
Hamtaro
▴ 10
1
vote
6
replies
262
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
5 hours ago by
CTLong
▴ 10
1
vote
5
replies
203
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 10 hours ago by
ATpoint
78k • written 13 hours ago by
singhankit973
• 0
0
votes
5
replies
227
views
How to deeply sequence long inserts
NGS
phage
read
display
Long
updated 1 hour ago by
GenoMax
136k • written 19 hours ago by
Ryan
• 0
3
votes
5
replies
489
views
Circular genome browser
genome-browser
circular-genome
updated 19 hours ago by
cmdcolin
★ 3.4k • written 27 days ago by
giammafer
▴ 20
0
votes
5
replies
228
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
updated just now by
dthorbur
▴ 860 • written 1 day ago by
tw_140
• 0
1
vote
4
replies
219
views
Bowtie mapping for single_end read
bowtie
16 hours ago by
Rita
• 0
4
votes
4
replies
1.9k
views
How to do simple pathway analysis?
rna-seq
genome
gene
updated 17 hours ago by
he1k
• 0 • written 4.5 years ago by
Seq225
▴ 110
3
votes
4
replies
175
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
Nitin Narwade
★ 1.5k • written 11 hours ago by
RNAseqer
▴ 250
2
votes
4
replies
341
views
Human mitochondrial reference genome
reference
genome
mitochondria
13 hours ago by
singhankit973
• 0
1
vote
4
replies
215
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
updated 17 hours ago by
GenoMax
136k • written 1 day ago by
Jimmy
▴ 10
1
vote
3
replies
205
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 15 hours ago by
Nitin Narwade
★ 1.5k • written 22 hours ago by
Bine
▴ 50
5
votes
3
replies
209
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
updated 15 hours ago by
Brian Bushnell
19k • written 1 day ago by
jiyoung
▴ 20
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 14 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
0
votes
3
replies
131
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 5 hours ago by
GenoMax
136k • written 7 hours ago by
cee28
• 0
0
votes
3
replies
137
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated just now by
ATpoint
78k • written 12 hours ago by
DINESHR
• 0
3
votes
2
replies
140
views
Moving AF tag to new column in a VCF file
mutect2
vcf
13 hours ago by
Christian
▴ 30
0
votes
2
replies
152
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 11 hours ago by
dsull
★ 5.0k • written 18 hours ago by
sehriban.buyukkilic
• 0
0
votes
2
replies
179
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 9 hours ago by
cmdcolin
★ 3.4k • written 10 hours ago by
Dylan C-C
• 0
3
votes
2
replies
628
views
CPTAC data, download, merge
CPTAC
merging
seq
data
RNA
updated 23 hours ago by
Mohita
▴ 50 • written 16 months ago by
Rob
▴ 160
0
votes
2
replies
284
views
Help doing differential expression analysis -experimental design and gProfiler TF interpretation-
gProfiler
mRNA
Differential-expression
TCGA
updated 4 hours ago by
rajabolacuan
• 0 • written 7 days ago by
Camilo Andres
▴ 40
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 3 hours ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
0
votes
2
replies
70
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 1 hour ago by
DBScan
▴ 200 • written 4 hours ago by
applepie
• 0
0
votes
2
replies
118
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
updated 1 hour ago by
GenoMax
136k • written 1 day ago by
cook.675
▴ 200
0
votes
2
replies
154
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
13 hours ago by
harter-ainsworth.izaak
• 0
0
votes
1
reply
90
views
VCF conservation into Treemix
Treemix
Plink
VCF
updated 14 hours ago by
singh.vijender
▴ 90 • written 15 hours ago by
reza
▴ 300
2
votes
1
reply
121
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 21 hours ago by
barslmn
★ 2.0k • written 1 day ago by
jiyoung
▴ 20
0
votes
1
reply
117
views
The difference blastn output when using subject and db options
genome
blastn
mite
annotation
tracker
updated 21 hours ago by
GenoMax
136k • written 1 day ago by
praasu
▴ 40
0
votes
1
reply
95
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 8 hours ago by
rpolicastro
12k • written 9 hours ago by
O.rka
▴ 710
0
votes
1
reply
49
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 6 minutes ago by
rpolicastro
12k • written 6 hours ago by
saipra003
▴ 10
0
votes
1
reply
260
views
FVA on Sybil
R
Sybil
metabolic
fba
fva
updated 1 hour ago by
Thomas
• 0 • written 22 months ago by
isM15
• 0
0
votes
1
reply
112
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 21 hours ago by
barslmn
★ 2.0k • written 23 hours ago by
Saurabh
• 0
0
votes
1
reply
90
views
bam or VCF files from GSE75010
bam
file
or
VCF
updated 13 hours ago by
ATpoint
78k • written 14 hours ago by
ahonya
• 0
1
vote
1
reply
135
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 14 hours ago by
singh.vijender
▴ 90 • written 23 hours ago by
DareDevil
★ 3.3k
2
votes
1
reply
223
views
EnhancedVolcano underrepresenting DEGs
R
updated 20 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
0
votes
0
replies
44
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
7 hours ago by
Richard Fontaine
• 0
0
votes
0
replies
61
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
16 hours ago by
rbronste
▴ 420
0
votes
0
replies
6
views
Blastn DB issue
cgmlst
blastn
5 minutes ago by
hakhasan
• 0
0
votes
0
replies
92
views
Bcftools consensus when reference is a deletion
consensus
vcf
13 hours ago by
selplat21
▴ 20
0
votes
0
replies
53
views
How to find node Postion and source(sample) ?
vg
6 hours ago by
zhang yi xing
▴ 20
42 results • Page
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Deeptools plotPCA on RNA-seq help
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
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Recent Replies
Comment: How to create a mutation frequency comparison plot?
by
rpolicastro
12k
You can make this with just ggplot. It would be two `geom_point`, a `geom_segment`, and two `geom_text` layers.
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
GenoMax
136k
> I run a blast with the sequences and most of them belongs to globin. Globin reads shown in your FastQC report are not going to add up to…
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
kvn95ss
▴ 20
Almost all your samples have the over represented sequence, you can blast the top 10 recurring sequences and see what it could be.
Comment: How to deeply sequence long inserts
by
GenoMax
136k
Linked read kits have not been offered by 10x genomics from last 3-4 years so that is not an option. Illumina now offers a long read tech…
Comment: Viral genes not showing up in combined mouse+virus alignment
by
GenoMax
136k
Try taking out the additional header lines from the combined GTF file. `NC_005089.1` lines should be immediately followed by `NC_001846.1` …
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
Nitin Narwade
★ 1.5k
Hmmmmm, okay. In this case I could think of another workaround, instead of drawing line/marks, you can add another modality to your plot, …
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
Hamtaro
▴ 10
I added the fastQC. What do you think of the possible cause I have proposed?
Comment: Problem in installing 'magick' R package
by
Jean-Karim Heriche
26k
This isn't a bioinformatics question. What do you mean by "install all the dependencies"? Did you read the error message? It's telling you …
Comment: Problem in installing 'magick' R package
by
DBScan
▴ 200
Have you read the error message? it tells you to try installing the Magick++ library: ``` Try installing: deb: libmagick++-dev (Debian, …
Answer: FVA on Sybil
by
Thomas
• 0
The first half of this vector should be your minimal fluxes per reaction and the second half your maximal fluxes per reaction. Thus this ve…
Comment: AttributeError: module 'collections' has no attribute 'Hashable'
by
jiyoung
▴ 20
Currently I am experiencing the same problem. Have you solved this?
Comment: Help doing differential expression analysis -experimental design and gProfiler T
by
rajabolacuan
• 0
Good Information Sir
Comment: Viral genes not showing up in combined mouse+virus alignment
by
cook.675
▴ 200
Hello I was curious to follow up and wonder if anyone knew why the viral genes are not showing up in the count matrix? I can't seem to solv…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
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