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117 results • Page
2 of 3
Sort: Votes
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Votes
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0
votes
1
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125
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
0
replies
85
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
2
replies
155
views
Error with goodSamplesGenes()
R
WGCNA
1 day ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
108
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
1
reply
133
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
2
replies
165
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
1 day ago by
Ankit
▴ 500
0
votes
7
replies
324
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
0
replies
100
views
doing some ontology enrichment analysis
GO
1 day ago by
aleksk779
• 0
0
votes
2
replies
164
views
novel and know mir156 and mir172
a
updated 1 day ago by
gayachit
▴ 200 • written 1 day ago by
Fadmo
• 0
0
votes
0
replies
89
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
1 day ago by
Chris
▴ 260
0
votes
0
replies
93
views
In scRNA, How should I set QC standards?
scRNA
QC
1 day ago by
mnx0723
• 0
0
votes
0
replies
85
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
1 day ago by
liuyibin2005
• 0
0
votes
0
replies
72
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
23 hours ago by
blur
▴ 280
0
votes
8
replies
419
views
STAR aligner options
STAR
23 hours ago by
theophile
• 0
0
votes
0
replies
76
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
23 hours ago by
Broccoli
• 0
0
votes
4
replies
245
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
22 hours ago by
rohitsatyam102
▴ 840
0
votes
9
replies
462
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 21 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
0
votes
0
replies
98
views
Training
chip-seq
ScATAC-seq
21 hours ago by
Manhezz
• 0
0
votes
0
replies
71
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 19 hours ago by
Ram
43k • written 1 day ago by
M'zelle
• 0
0
votes
1
reply
96
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 19 hours ago by
Ram
43k • written 19 hours ago by
chiditatawmbi
• 0
0
votes
0
replies
60
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
18 hours ago by
alenew.am
• 0
0
votes
0
replies
65
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 18 hours ago by
Ram
43k • written 18 hours ago by
Tolga
▴ 20
0
votes
1
reply
119
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 18 hours ago by
Ram
43k • written 19 hours ago by
Picasa
▴ 640
0
votes
3
replies
353
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
18 hours ago by
Nitin
• 0
0
votes
0
replies
78
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 18 hours ago by
Ram
43k • written 20 hours ago by
udakshi
• 0
0
votes
5
replies
317
views
Parsing fasta file by coordinates
linux
fasta
updated 16 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
0
votes
1
reply
73
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 16 hours ago by
GenoMax
140k • written 16 hours ago by
David Tachiquín
• 0
0
votes
1
reply
97
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 15 hours ago by
Ram
43k • written 23 hours ago by
Christian
• 0
0
votes
1
reply
89
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 11 hours ago by
Pierre Lindenbaum
160k • written 11 hours ago by
ekirsch
• 0
0
votes
9
replies
289
views
Low number of both surviving reads after trimming
trimmomatic
trimming
10 hours ago by
Jay
• 0
0
votes
2
replies
119
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 10 hours ago by
Mensur Dlakic
★ 26k • written 13 hours ago by
Harrison
• 0
0
votes
4
replies
200
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
10 hours ago by
BRENO
• 0
0
votes
0
replies
38
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
10 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
26
views
Convert to ENTREZGENE
maize
ENTREZGENE
7 hours ago by
sansan_96
▴ 50
0
votes
0
replies
19
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
4 hours ago by
analyst
▴ 10
0
votes
0
replies
20
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
3 hours ago by
pavithraashokkumar818
• 0
0
votes
0
replies
16
views
Alignment with new reference
alignment
1 hour ago by
marco.barr
▴ 30
0
votes
1
reply
18
views
Mapping ortholog human and mouse transcript
biomart
updated just now by
manaswwm
▴ 490 • written 2 hours ago by
1769mkc
★ 1.2k
0
votes
0
replies
165
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
6 days ago by
Apex92
▴ 280
0
votes
0
replies
1
view
How do I get the gene annotations as a text file from a genebank file?
genebank
sequence-annotation
just now by
En Xin
• 0
0
votes
0
replies
156
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
6 days ago by
mb
• 0
0
votes
0
replies
164
views
working with shapeit.
shapeit
6 days ago by
sanchit000singhdr098
• 0
0
votes
3
replies
298
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
6 days ago by
kabir.deb
▴ 80
0
votes
5
replies
407
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
6 days ago by
Learner
• 0
0
votes
0
replies
178
views
Only positive enrichment score in GSEA
enrichmentanalysis
clusterprofiler
gsea
bioconductor
rnaseq
6 days ago by
enee
▴ 10
0
votes
1
reply
227
views
PCA script correction
correction
script
PCA
updated 6 days ago by
BioinfGuru
★ 1.6k • written 6 days ago by
prity6459
• 0
0
votes
1
reply
203
views
Getting error in alignment using STAR
STAR
Error
updated 5 days ago by
Michael
54k • written 5 days ago by
pavithra.bioinformatics
• 0
0
votes
0
replies
148
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
5 days ago by
asmariyaz23
▴ 10
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
5 days ago by
rheab1230
▴ 140
117 results • Page
2 of 3
Recent Votes
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Recent Awards •
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Teacher
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160k
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brian.fristensky
▴ 460
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★ 2.4k
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amitpande74
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beacamara
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Recent Replies
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
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.
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