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72 results • Page
2 of 2
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Views
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0
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122
views
Creating heatmap for ChIP-seq using deeptools
heatmap
chipseq
chip
deeptools
visualization
6 days ago by
biology_inform
▴ 50
0
votes
0
replies
6
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
14 minutes ago by
cee28
• 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
148
views
not best k value found
de
assemblly
assembly
novo
kmergenie
4 days ago by
shaileshdesai76
• 0
0
votes
0
replies
790
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
163
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
5 days ago by
pl23
• 0
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
1
vote
0
replies
134
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
5 days ago by
WUSCHEL
▴ 720
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
0
replies
106
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
6 days ago by
Ngrin
• 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
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
116
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
6 days ago by
turcoa1
• 0
0
votes
0
replies
98
views
Harmony integration PC variance explained
scRNA
integration
harmony
1 day ago by
e.iich
• 0
0
votes
0
replies
92
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
1 day ago by
Jaykishan
• 0
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
0
replies
123
views
TF Footprinting using HINT ATAC module from RGT
hintatac
footprinting
rgttoolbox
atacseq
6 days ago by
alphaflylizard
• 0
1
vote
0
replies
74
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
1 day ago by
joe
▴ 390
0
votes
0
replies
78
views
missing region in the process of annotation
annotatr
minfi
1 day ago by
Aki
▴ 10
0
votes
0
replies
62
views
String App in Cytoscape
App
String
cytoscape
23 hours ago by
hellokwmin
• 0
0
votes
0
replies
113
views
Trouble making a ggmsa alignment plot
R
ggmsa
6 days ago by
andre.arrudalima
▴ 30
72 results • Page
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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:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
Extract UMIs using UMI-tools
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Recent Replies
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.
Answer: Generate Read counts from bam file
by
Enrique
• 0
Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
Comment: How to deeply sequence long inserts
by
Brian Bushnell
19k
Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
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