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1,000 results • Page
1 of 20
Sort: Rank
Rank
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Votes
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0
votes
0
replies
1
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Synthetic lethality and cancer database
interaction
lethal
synthetic
just now by
Shicheng Guo
★ 9.4k
0
votes
0
replies
15
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
1 hour ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
55
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 2 hours ago by
Pierre Lindenbaum
160k • written 3 hours ago by
ekirsch
• 0
0
votes
4
replies
114
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
1 hour ago by
BRENO
• 0
0
votes
2
replies
86
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 2 hours ago by
Mensur Dlakic
★ 26k • written 5 hours ago by
Harrison
• 0
0
votes
0
replies
49
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
7 hours ago by
sithlordashley
• 0
0
votes
1
reply
57
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 7 hours ago by
GenoMax
140k • written 8 hours ago by
David Tachiquín
• 0
0
votes
9
replies
249
views
Low number of both surviving reads after trimming
trimmomatic
trimming
2 hours ago by
Jay
• 0
0
votes
1
reply
74
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
updated 7 hours ago by
GenoMax
140k • written 9 hours ago by
Mohamed Abderrahmane
▴ 10
2
votes
2
replies
83
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
9 hours ago by
DYLAN NICO
• 0
0
votes
0
replies
51
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 9 hours ago by
Ram
43k • written 9 hours ago by
Tolga
▴ 20
0
votes
0
replies
45
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
9 hours ago by
alenew.am
• 0
0
votes
3
replies
281
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
9 hours ago by
Nitin
• 0
0
votes
1
reply
80
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 10 hours ago by
Ram
43k • written 10 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
104
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 9 hours ago by
Ram
43k • written 11 hours ago by
Picasa
▴ 640
0
votes
0
replies
62
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 9 hours ago by
Ram
43k • written 12 hours ago by
udakshi
• 0
0
votes
0
replies
80
views
Training
chip-seq
ScATAC-seq
12 hours ago by
Manhezz
• 0
1
vote
2
replies
111
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 8 hours ago by
Ram
43k • written 13 hours ago by
gdfsnkfns
• 0
1
vote
11
replies
292
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 7 hours ago by
GenoMax
140k • written 13 hours ago by
Lila M
★ 1.2k
2
votes
2
replies
106
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 8 hours ago by
dariober
14k • written 14 hours ago by
Pumla
• 0
0
votes
1
reply
82
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 6 hours ago by
Ram
43k • written 14 hours ago by
Christian
• 0
0
votes
0
replies
61
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
15 hours ago by
Broccoli
• 0
0
votes
0
replies
59
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
15 hours ago by
blur
▴ 280
0
votes
0
replies
67
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
16 hours ago by
liuyibin2005
• 0
0
votes
0
replies
56
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 10 hours ago by
Ram
43k • written 16 hours ago by
M'zelle
• 0
0
votes
0
replies
75
views
In scRNA, How should I set QC standards?
scRNA
QC
19 hours ago by
mnx0723
• 0
0
votes
0
replies
75
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
22 hours ago by
Chris
▴ 260
2
votes
10
replies
713
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 10 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
0
replies
90
views
doing some ontology enrichment analysis
GO
1 day ago by
aleksk779
• 0
0
votes
2
replies
161
views
novel and know mir156 and mir172
a
updated 1 day ago by
gayachit
▴ 200 • written 1 day ago by
Fadmo
• 0
2
votes
8
replies
258
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
0
votes
8
replies
417
views
STAR aligner options
STAR
15 hours ago by
theophile
• 0
0
votes
2
replies
163
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
1 day ago by
Ankit
▴ 500
0
votes
1
reply
106
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 1 day ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
0
replies
81
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 1 day ago by
Ram
43k • written 1 day ago by
r.shiasi3897
▴ 10
0
votes
0
replies
82
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
1
reply
121
views
How can I remove duplicate SNP?
plink
updated 1 day ago by
iraun
6.2k • written 1 day ago by
Zhennan
• 0
0
votes
1
reply
131
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 1 day ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
0
replies
76
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
0
replies
79
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
0
votes
0
replies
85
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
3
replies
216
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
0
votes
2
replies
153
views
Error with goodSamplesGenes()
R
WGCNA
1 day ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
92
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
7
replies
318
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 1 day ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
1
reply
145
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
1
reply
142
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 1 day ago by
David Arturo
• 0
0
votes
0
replies
104
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
1 day ago by
kiraqueen
• 0
2
votes
2
replies
212
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 2 days ago by
fred.s.kremer
▴ 110
0
votes
0
replies
101
views
Convert VCF file and add covariate information
VCF
PED
PLINK
2 days ago by
asmariyaz23
▴ 10
1,000 results • Page
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Answer: log2(TPM+1)
Comment: Error in openning FastQC
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160k
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beacamara
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Recent Replies
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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