Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
72 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
9
votes
16
replies
673
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
9 hours ago by
analyst
▴ 10
2
votes
8
replies
580
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
1
vote
6
replies
486
views
frequency plot for peaks
chip-seq
chipseeker
updated 6 hours ago by
Ankit
▴ 400 • written 15 days ago by
Mehwish
▴ 10
2
votes
6
replies
2.1k
views
No best K value found
Assembly
Kmergenie
updated 4 days ago by
shaileshdesai76
• 0 • written 6.8 years ago by
kspata
▴ 80
1
vote
6
replies
247
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
3 hours ago by
CTLong
▴ 10
0
votes
6
replies
491
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4
bwa-mem
target-capture-sequencing
alignment
6 days ago by
Miguel
• 0
1
vote
4
replies
217
views
Bowtie mapping for single_end read
bowtie
14 hours ago by
Rita
• 0
1
vote
4
replies
290
views
Analyze with Geo2R
R
NCBI
4 days ago by
anasjamshed
▴ 120
0
votes
4
replies
224
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
15 hours ago by
tw_140
• 0
0
votes
4
replies
235
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
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 6 days ago by
ayaosama2111
▴ 10 • written 7.0 years ago by
Nicolas Rosewick
10k
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
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 2 days ago by
Cibo
• 0 • written 2.0 years ago by
Amina
• 0
0
votes
3
replies
211
views
merged rs number information
merged
dbsnp
1 day ago by
sskimvd
• 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
3
replies
115
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 3 hours ago by
GenoMax
136k • written 5 hours ago by
cee28
• 0
1
vote
3
replies
150
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 6 hours ago by
dsull
★ 5.0k • written 9 hours ago by
RNAseqer
▴ 250
0
votes
3
replies
295
views
Annovar - Annotated file cells show string
annovar
4 days ago by
Roshan
• 0
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 12 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
1
vote
3
replies
201
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 13 hours ago by
Nitin Narwade
★ 1.5k • written 20 hours ago by
Bine
▴ 50
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 1 hour ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
3
votes
2
replies
231
views
t-test by row
R
t-test
updated 6 days ago by
dthorbur
▴ 860 • written 7 days ago by
sooni
▴ 10
0
votes
2
replies
254
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation
Variant
proteomics
FASTA
VCF
5 days ago by
chscho
• 0
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 6 days ago by
manaswiniparija3
▴ 10
1
vote
2
replies
280
views
Wrong in Deeptools : the enrichment of TSS and TES region are similar when using scale-region
plotprofile
computematrix
Deeptools
scale-region
5 days ago by
hao
• 0
0
votes
2
replies
264
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
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
2
votes
2
replies
571
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment
scDblFinder
SMART-Seq
updated 1 day ago by
e.r.zakiev
▴ 170 • written 5 months ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
196
views
how to use pilon
genome
pipelines
assembly
pilon
contig
updated 1 day ago by
Arup Ghosh
3.2k • written 7 days ago by
vasudhapai
• 0
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
1 day ago by
je71xusa
• 0
0
votes
2
replies
158
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 7 hours ago by
cmdcolin
★ 3.4k • written 8 hours ago by
Dylan C-C
• 0
0
votes
1
reply
234
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 3 days ago by
GenoMax
136k • written 4 days ago by
subhiksha
• 0
0
votes
1
reply
132
views
error in plink
polygenicriskscore
prscalculation
prs
plink
error
updated 6 days ago by
biofalconch
★ 1.1k • written 6 days ago by
Emilija
• 0
0
votes
1
reply
110
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 19 hours ago by
barslmn
★ 2.0k • written 21 hours ago by
Saurabh
• 0
0
votes
1
reply
88
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 7 hours ago by
O.rka
▴ 710
2
votes
1
reply
118
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 19 hours ago by
barslmn
★ 2.0k • written 23 hours ago by
jiyoung
▴ 20
2
votes
1
reply
222
views
EnhancedVolcano underrepresenting DEGs
R
updated 18 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
1
vote
1
reply
226
views
Eigen_phred_coding values interpretation
variation
SNP
annotation
6 days ago by
Lukas
▴ 40
1
vote
1
reply
148
views
Beginner differential methylation analysis
Methylation
updated 2 days ago by
Basti
★ 1.8k • written 2 days ago by
a.basitkhan1990
▴ 30
0
votes
1
reply
181
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
1
vote
1
reply
516
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 2 days ago by
tingting
▴ 10 • written 7 months ago by
Chris
▴ 230
1
vote
1
reply
839
views
cellphonedb results visualization
cellphonedb
ktplotspy
cpdb
visulization
updated 6 days ago by
miguellarrazlopezdenovales
▴ 20 • written 10 months ago by
piotto
▴ 20
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
68
views
String App in Cytoscape
App
String
cytoscape
1 day ago by
hellokwmin
• 0
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
0
replies
71
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
1 day ago by
Smriti
▴ 10
0
votes
0
replies
32
views
Problem in installing 'magick' R package
R
installation
package
magick
2 hours ago by
applepie
• 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
812
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
59
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
14 hours ago by
rbronste
▴ 420
72 results • Page
1 of 2
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:
Recent Locations •
All
Chengdu,
3 minutes ago
Ramat Gan,
4 minutes ago
WCIP | Glasgow | UK,
8 minutes ago
France,
13 minutes ago
United States,
13 minutes ago
Hong Kong,
14 minutes ago
Frankrike,
14 minutes ago
Recent Awards •
All
Popular Question
to
applepie
• 0
Popular Question
to
saipra003
▴ 10
Popular Question
to
O.rka
▴ 710
Popular Question
to
Daniel
▴ 30
Popular Question
to
prasundutta87
▴ 660
Popular Question
to
RNAseqer
▴ 250
Scholar
to
Devon Ryan
104k
Recent Replies
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
Answer: 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.
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?
Traffic: 1672 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6