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48 results • Page
1 of 1
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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 3 hours ago by
doggie
• 0 • written 6.2 years ago by
Anushka
▴ 20
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 13 hours ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
3
votes
2
replies
939
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 3 hours ago by
el24
▴ 40 • written 2.0 years ago by
emmah
• 0
9
votes
16
replies
685
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
21 hours ago by
analyst
▴ 10
1
vote
6
replies
496
views
frequency plot for peaks
chip-seq
chipseeker
updated 18 hours ago by
Ankit
▴ 400 • written 16 days ago by
Mehwish
▴ 10
2
votes
4
replies
344
views
Human mitochondrial reference genome
reference
genome
mitochondria
22 hours ago by
singhankit973
• 0
0
votes
1
reply
327
views
How to use conumee segment mean for gistic input
genomics
gistic
NGS
methylation
conumee
updated 5 hours ago by
sativus
▴ 10 • written 14 months ago by
Thind amarinder
▴ 340
1
vote
7
replies
324
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts
HISAT2
RNA-seq
9 hours ago by
Hamtaro
▴ 10
0
votes
6
replies
304
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
2 hours ago by
tw_140
• 0
0
votes
1
reply
303
views
FVA on Sybil
R
Sybil
metabolic
fba
fva
updated 11 hours ago by
Thomas
• 0 • written 22 months ago by
isM15
• 0
0
votes
2
replies
302
views
Help doing differential expression analysis -experimental design and gProfiler TF interpretation-
gProfiler
mRNA
Differential-expression
TCGA
updated 13 hours ago by
rajabolacuan
• 0 • written 7 days ago by
Camilo Andres
▴ 40
4
votes
6
replies
299
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 3 hours ago by
i.sudbery
18k • written 1 day ago by
sehriban.buyukkilic
• 0
1
vote
6
replies
295
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
14 hours ago by
CTLong
▴ 10
0
votes
3
replies
282
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 23 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
0
votes
2
replies
280
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 19 hours ago by
cmdcolin
★ 3.4k • written 19 hours ago by
Dylan C-C
• 0
0
votes
5
replies
278
views
How to deeply sequence long inserts
NGS
phage
read
display
Long
updated 10 hours ago by
GenoMax
136k • written 1 day ago by
Ryan
• 0
3
votes
6
replies
258
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 2 hours ago by
NextGenSeek
• 0 • written 22 hours ago by
singhankit973
• 0
3
votes
4
replies
243
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 10 hours ago by
Nitin Narwade
★ 1.5k • written 21 hours ago by
RNAseqer
▴ 250
0
votes
3
replies
195
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 9 hours ago by
ATpoint
78k • written 21 hours ago by
DINESHR
• 0
4
votes
7
replies
193
views
regarding blast result interpretation
blast
updated 5 hours ago by
dthorbur
▴ 870 • written 7 hours ago by
Raman
• 0
2
votes
5
replies
191
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 52 minutes ago by
tshtatland
▴ 170 • written 17 hours ago by
cee28
▴ 20
0
votes
2
replies
174
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
updated 10 hours ago by
GenoMax
136k • written 1 day ago by
cook.675
▴ 200
0
votes
2
replies
173
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
23 hours ago by
harter-ainsworth.izaak
• 0
1
vote
1
reply
167
views
Match variants for allele frequency, LD score, and other features
snp
3 hours ago by
Jautis
▴ 520
1
vote
1
reply
157
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 23 hours ago by
singh.vijender
▴ 100 • written 1 day ago by
DareDevil
★ 3.3k
3
votes
2
replies
155
views
Moving AF tag to new column in a VCF file
mutect2
vcf
22 hours ago by
Christian
▴ 30
1
vote
2
replies
146
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 10 hours ago by
DBScan
▴ 210 • written 14 hours ago by
applepie
• 0
0
votes
1
reply
145
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 7 hours ago by
CTLong
▴ 10 • written 2 days ago by
e.iich
• 0
0
votes
4
replies
142
views
Making multiple box plots with relative abundance in R
R
Boxplots
4 hours ago by
ohtang7
▴ 30
1
vote
1
reply
131
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 6 hours ago by
rpolicastro
12k • written 18 hours ago by
O.rka
▴ 710
0
votes
0
replies
125
views
Mapping Mouse RNAseq Marker Genes to Reactome Pathways
single-cell
pathways
reactome
RNAseq
gene
1 hour ago by
el24
▴ 40
2
votes
2
replies
120
views
Blastn DB issue
cgmlst
blastn
8 hours ago by
hakhasan
• 0
0
votes
1
reply
117
views
bam or VCF files from GSE75010
bam
file
or
VCF
updated 22 hours ago by
ATpoint
78k • written 23 hours ago by
ahonya
• 0
0
votes
1
reply
116
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 7 hours ago by
rpolicastro
12k • written 15 hours ago by
saipra003
▴ 10
0
votes
0
replies
111
views
Bcftools consensus when reference is a deletion
consensus
vcf
23 hours ago by
selplat21
▴ 20
0
votes
1
reply
102
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
updated 6 hours ago by
Nitin Narwade
★ 1.5k • written 8 hours ago by
eamaunders
• 0
1
vote
1
reply
97
views
Two identical reads in my bam files but with a different in CIGAR are mapped in a different location in IGV
pysam
6 hours ago by
ManuelDB
▴ 80
1
vote
2
replies
77
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 3 hours ago by
ATpoint
78k • written 4 hours ago by
ohtang7
▴ 30
0
votes
2
replies
76
views
What type of cancer did they study in this paper?
cancer
RNAseq
single-cell
updated 3 hours ago by
GenoMax
136k • written 3 hours ago by
JACKY
▴ 120
0
votes
0
replies
75
views
How to find node Postion and source(sample) ?
vg
16 hours ago by
zhang yi xing
▴ 20
0
votes
0
replies
69
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
16 hours ago by
Richard Fontaine
• 0
0
votes
0
replies
47
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
5 hours ago by
reaset41
• 0
0
votes
0
replies
46
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 5 hours ago by
GenoMax
136k • written 5 hours ago by
PierreGT
• 0
0
votes
0
replies
39
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
6 hours ago by
jorge.cortes.miranda
• 0
0
votes
0
replies
38
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
3 hours ago by
aheinzel
▴ 130
0
votes
0
replies
37
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 3 hours ago by
GenoMax
136k • written 4 hours ago by
sativus
▴ 10
0
votes
0
replies
12
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
1 hour ago by
tss243
• 0
0
votes
0
replies
7
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
2 minutes ago by
Bryan
▴ 10
48 results • Page
1 of 1
Recent Votes
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
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
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Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
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
▴ 170
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.
Answer: 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?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
Comment: p-value combination methods
by
i.sudbery
18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
ATpoint
78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping
by
doggie
• 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
dthorbur
▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
Comment: Making multiple box plots with relative abundance in R
by
ohtang7
▴ 30
Thank you!! I really appreciate your help.
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