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115 results • Page
2 of 3
Sort: replies
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Votes
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0
votes
1
reply
140
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 3 days ago by
Ram
43k • written 3 days ago by
Sony
▴ 10
0
votes
1
reply
149
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 3 days ago by
zx8754
11k • written 3 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
1
reply
148
views
Karytotype color annotations
karyotype
annotations
chromosome
color
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
Mary
• 0
0
votes
1
reply
162
views
MACS3 or SEACR
MACS3
SEACR
updated 2 days ago by
jared.andrews07
★ 16k • written 2 days ago by
daffodil
▴ 10
1
vote
1
reply
154
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 2 days ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
0
votes
1
reply
142
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 2 days ago by
ATpoint
81k • written 2 days ago by
David Arturo
• 0
0
votes
1
reply
148
views
dbsnp flanks information
dbsnp
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
sskimvd
• 0
0
votes
1
reply
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
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
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
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 20 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
119
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 19 hours ago by
Ram
43k • written 20 hours ago by
Picasa
▴ 640
0
votes
1
reply
97
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 15 hours ago by
Ram
43k • written 1 day ago by
Christian
• 0
0
votes
1
reply
89
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 12 hours ago by
Pierre Lindenbaum
160k • written 12 hours ago by
ekirsch
• 0
0
votes
1
reply
24
views
Mapping ortholog human and mouse transcript
biomart
updated 37 minutes ago by
manaswwm
▴ 490 • written 2 hours ago by
1769mkc
★ 1.2k
1
vote
0
replies
34
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
9 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
85
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq
Somatic-Mutation
Variant-Calling
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Sharon
▴ 600
0
votes
0
replies
115
views
Visium dataset distance between spots calculations
SpatialSeq
Visium
updated 2 days ago by
GenoMax
140k • written 2 days ago by
houssi301
• 0
0
votes
0
replies
27
views
Convert to ENTREZGENE
maize
ENTREZGENE
7 hours ago by
sansan_96
▴ 50
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
19
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
4 hours ago by
analyst
▴ 10
0
votes
0
replies
1.1k
views
Effect of dbSNP build differences in variant calling
GRCh38
dbSNP
variant-calling
GATK
assembly
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
0
votes
0
replies
843
views
Variant quality scores with different variant caller: HaplotypeCaller vs DeepVariant. How to interpret the quality scores?
variant-calling
DeepVariant
HaplotypeCaller
quality-score
updated 2 days ago by
Ram
43k • written 2.4 years ago by
Jordi
▴ 50
0
votes
0
replies
362
views
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
Variant-Calling
updated 2 days ago by
Ram
43k • written 2.2 years ago by
jeni
▴ 90
0
votes
0
replies
100
views
doing some ontology enrichment analysis
GO
1 day ago by
aleksk779
• 0
0
votes
0
replies
336
views
Benchmarking pipeline for Variant identification using RNA-seq data
RNA-seq
somatic
Variant-calling
germline
updated 2 days ago by
Ram
43k • written 17 months ago by
ahkam.s
• 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
86
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
1 day ago by
blur
▴ 280
0
votes
0
replies
98
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
2 days ago by
Adrian Pelin
★ 2.6k
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
1 day ago by
Broccoli
• 0
0
votes
0
replies
106
views
t2t Reference gtf file
t2t
3 days ago by
Emre
• 0
0
votes
0
replies
109
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
3 days ago by
Yingying
• 0
0
votes
0
replies
98
views
Training
chip-seq
ScATAC-seq
21 hours ago by
Manhezz
• 0
0
votes
0
replies
84
views
Metacoder plot_cladogram long calculation times
Metacoder
updated 3 days ago by
Ram
43k • written 3 days ago by
La52dA97b6
• 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
0
replies
21
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
4 hours ago by
pavithraashokkumar818
• 0
0
votes
0
replies
60
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
19 hours ago by
alenew.am
• 0
0
votes
0
replies
65
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 19 hours ago by
Ram
43k • written 19 hours ago by
Tolga
▴ 20
0
votes
0
replies
18
views
Alignment with new reference
alignment
1 hour ago by
marco.barr
▴ 30
0
votes
0
replies
105
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
PBC
▴ 10
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 21 hours ago by
udakshi
• 0
0
votes
0
replies
88
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
3 days ago by
erbrocato
• 0
0
votes
0
replies
97
views
OSCC Dataset downlod using TCGA biolink
R
OSSC
TCGAbiolink
GDC
updated 3 days ago by
Ram
43k • written 4 days ago by
Biogeek
• 0
0
votes
0
replies
104
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 3 days ago by
Ram
43k • written 3 days ago by
barrypraveen
▴ 130
1
vote
0
replies
97
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
3 days ago by
mrazib0210
▴ 10
1
vote
0
replies
109
views
checkm lineage.ms output file
checkm
lineage
4 days ago by
A_heath
▴ 160
0
votes
0
replies
99
views
What is the usual basecalls length and reference mapping length relationship?
genome
alignment
rna-seq
updated 4 days ago by
Carlo Yague
8.6k • written 4 days ago by
anne
• 0
115 results • Page
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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!
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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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