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326 results • Page
1 of 7
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
11
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
50 minutes ago by
saipra003
▴ 10
0
votes
0
replies
17
views
How to find node Postion and source(sample) ?
vg
1 hour ago by
zhang yi xing
▴ 20
0
votes
0
replies
20
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
2 hours ago by
Richard Fontaine
• 0
0
votes
3
replies
57
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 38 minutes ago by
GenoMax
136k • written 2 hours ago by
cee28
• 0
0
votes
1
reply
71
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 3 hours ago by
rpolicastro
12k • written 4 hours ago by
O.rka
▴ 710
0
votes
2
replies
115
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 4 hours ago by
cmdcolin
★ 3.4k • written 5 hours ago by
Dylan C-C
• 0
1
vote
3
replies
127
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 3 hours ago by
dsull
★ 5.0k • written 6 hours ago by
RNAseqer
▴ 250
0
votes
0
replies
54
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
10 hours ago by
rbronste
▴ 420
1
vote
3
replies
194
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 10 hours ago by
Nitin Narwade
★ 1.5k • written 17 hours ago by
Bine
▴ 50
0
votes
1
reply
105
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 16 hours ago by
barslmn
★ 2.0k • written 18 hours ago by
Saurabh
• 0
1
vote
6
replies
174
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
20 minutes ago by
CTLong
▴ 10
2
votes
1
reply
112
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 16 hours ago by
barslmn
★ 2.0k • written 20 hours ago by
jiyoung
▴ 20
0
votes
0
replies
65
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
21 hours ago by
Smriti
▴ 10
1
vote
4
replies
212
views
Bowtie mapping for single_end read
bowtie
11 hours ago by
Rita
• 0
0
votes
0
replies
64
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
22 hours ago by
cook.675
▴ 200
0
votes
0
replies
64
views
String App in Cytoscape
App
String
cytoscape
1 day ago by
hellokwmin
• 0
0
votes
0
replies
82
views
missing region in the process of annotation
annotatr
minfi
1 day ago by
Aki
▴ 10
1
vote
0
replies
77
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
1 day ago by
joe
▴ 390
0
votes
4
replies
219
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
11 hours ago by
tw_140
• 0
9
votes
16
replies
668
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
6 hours ago by
analyst
▴ 10
0
votes
0
replies
85
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
1 day ago by
user230613
▴ 350
0
votes
4
replies
234
views
Species coverage in the NCBI protein NR database ?
NR
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
HERMAN
▴ 10
0
votes
0
replies
92
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
1 day ago by
Jaykishan
• 0
0
votes
0
replies
98
views
Harmony integration PC variance explained
scRNA
integration
harmony
1 day ago by
e.iich
• 0
0
votes
3
replies
210
views
merged rs number information
merged
dbsnp
1 day ago by
sskimvd
• 0
1
vote
1
reply
148
views
Beginner differential methylation analysis
Methylation
updated 1 day ago by
Basti
★ 1.8k • written 2 days ago by
a.basitkhan1990
▴ 30
2
votes
1
reply
222
views
EnhancedVolcano underrepresenting DEGs
R
updated 15 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
0
votes
0
replies
102
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
2 days ago by
jiazheng_lin
• 0
0
votes
0
replies
114
views
Negative F statistics for sex check in plink
plink
check
sex
2 days ago by
kl
▴ 10
0
votes
1
reply
180
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 1 day ago by
Arup Ghosh
3.2k • written 3 days ago by
Mehwish
▴ 10
0
votes
1
reply
234
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 3 days ago by
GenoMax
136k • written 3 days ago by
subhiksha
• 0
0
votes
3
replies
331
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 3 days ago by
ATpoint
78k • written 4 days ago by
manuelmourato25
• 0
0
votes
0
replies
221
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
4 days ago by
Wenke
• 0
0
votes
3
replies
295
views
Annovar - Annotated file cells show string
annovar
4 days ago by
Roshan
• 0
0
votes
1
reply
230
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 4 days ago by
GenoMax
136k • written 4 days ago by
Soumajit
▴ 40
0
votes
0
replies
153
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
4 days ago by
bioinfo
▴ 60
0
votes
0
replies
154
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
4 days ago by
kdca
• 0
0
votes
3
replies
266
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
4 days ago by
Sara
▴ 230
0
votes
0
replies
800
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
4 days ago by
Mark
• 0
0
votes
0
replies
149
views
not best k value found
de
assemblly
assembly
novo
kmergenie
4 days ago by
shaileshdesai76
• 0
0
votes
0
replies
158
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
5 days ago by
Carmen
• 0
0
votes
0
replies
164
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
5 days ago by
pl23
• 0
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
21 hours ago by
je71xusa
• 0
0
votes
2
replies
260
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 5 days ago by
Raony Guimarães
★ 1.3k • written 5 days ago by
ThePlaintiff
▴ 80
2
votes
8
replies
578
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
updated 1 day ago by
GenoMax
136k • written 7 days ago by
ian.will
▴ 10
5
votes
2
replies
235
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
4 days ago by
Rafael Soler
★ 1.2k
1
vote
2
replies
190
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 5 days ago by
WouterDeCoster
47k • written 5 days ago by
manaswiniparija3
▴ 10
1
vote
0
replies
134
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
6 days ago by
WUSCHEL
▴ 720
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 9 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
0
votes
0
replies
106
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
6 days ago by
Ngrin
• 0
326 results • Page
1 of 7
Recent Votes
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
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
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saipra003
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O.rka
▴ 710
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Recent Replies
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.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads
by
cee28
• 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
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 …
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