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 year
all time
today
this week
this month
this year
1,000 results • Page
3 of 20
Sort: Votes
Rank
Views
Votes
Replies
5
votes
10
replies
940
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
3 months ago by
alwayshope
▴ 40
5
votes
6
replies
603
views
normalize coordinates to the same length
r
genomicranges
8 months ago by
Chironex
▴ 40
5
votes
7
replies
632
views
About the value in bigwig file
ATAC-seq
updated 4 months ago by
rfran010
▴ 880 • written 4 months ago by
Chris
▴ 230
5
votes
7
replies
702
views
Salmon index not progressing
salmon
updated 10 weeks ago by
Michael
53k • written 10 weeks ago by
camillab.
▴ 150
5
votes
11
replies
918
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 3 months ago by
cmdcolin
★ 3.4k • written 3 months ago by
pablo
▴ 300
5
votes
6
replies
1.4k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools
bam
bed
updated 5 months ago by
Ram
41k • written 13 months ago by
Eliveri
▴ 350
5
votes
4
replies
1.0k
views
Running nf-core rnaseq with smart-seq3 data
smart-seq3
nf-core
nextflow
12 months ago by
firestar
★ 1.6k
5
votes
11
replies
3.4k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 8 months ago by
Ram
41k • written 5.6 years ago by
HG
▴ 30
5
votes
2
replies
716
views
how to loop through various dataframes in R
dataframe
R
updated 11 months ago by
zx8754
11k • written 11 months ago by
rheab1230
▴ 140
5
votes
5
replies
3.4k
views
Gencode annotation and read counting- how to handle overlapping/ambiguous features
gencode
alignment
RNA-Seq
updated 11 months ago by
Ram
41k • written 8.5 years ago by
Adamc
▴ 680
5
votes
8
replies
1.8k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 6 weeks ago by
Jingjingzhang
• 0 • written 3.3 years ago by
from the mountains
▴ 230
5
votes
8
replies
837
views
conda: command not found: gatk.
conda
gatk
5 months ago by
bestone
▴ 20
5
votes
12
replies
998
views
Data from an experiment
single-cell
updated 9 months ago by
GenoMax
136k • written 9 months ago by
Chris
▴ 230
5
votes
7
replies
3.3k
views
STAR aligner pauses frequently during mapping
rna-seq
STAR
updated 10 months ago by
Ram
41k • written 8.6 years ago by
E Chen
• 0
5
votes
2
replies
528
views
30 bp sequence that does not show hit within a genome
similarity
updated 11 months ago by
shenwei356
8.3k • written 11 months ago by
GR
▴ 400
5
votes
3
replies
370
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 11 weeks ago by
Ram
41k • written 11 weeks ago by
sarahmanderni
▴ 100
5
votes
3
replies
701
views
GENE code ID conversion
ensembl
entrez
8 months ago by
Confused_human
▴ 10
5
votes
7
replies
705
views
RNAseq analysis of phage infection - should I split the counts mapping to host/phage prior to normalization and analysis?
RNAseq
Prokaryotic
7 months ago by
Sean
▴ 10
5
votes
5
replies
2.2k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 4 weeks ago by
Feng Tian
▴ 20 • written 5.2 years ago by
gewa
▴ 20
5
votes
7
replies
813
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 6 months ago by
supernovamik
• 0 • written 3.9 years ago by
ee.mohseni.alert
▴ 50
5
votes
4
replies
1.8k
views
MyVariant.info fields descriptions?
genome
snp
variant
updated 8 months ago by
Ram
41k • written 7.5 years ago by
Nolwenn Lavielle
▴ 90
5
votes
6
replies
3.2k
views
Changes log2FC values of DESeq2
log2FC
DESeq2
updated 8 months ago by
Ram
41k • written 5.9 years ago by
realnewbie
▴ 30
5
votes
2
replies
494
views
I want to print only those lines which contain non repetitive amino acid sequences
Linux
python
awk
sed
updated 9 months ago by
Ram
41k • written 9 months ago by
muhammadhassam8
• 0
5
votes
5
replies
457
views
Counting 705 fasta header characters ('>') in human genome
human-genome
genetics
updated 5 weeks ago by
ATpoint
78k • written 5 weeks ago by
10mz1
• 0
5
votes
35
replies
3.0k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 4 months ago by
Jordan M Eizenga
▴ 410 • written 5 months ago by
anivlete
• 0
5
votes
8
replies
1.3k
views
snpeff install error
snpeff
updated 6 months ago by
Ram
41k • written 7 months ago by
bestone
▴ 20
5
votes
6
replies
1.0k
views
I can not allocate ram memory for WSL2
WSL2
8 months ago by
ailton
• 0
5
votes
4
replies
4.0k
views
Black color reads in IGV: bwa-meth
IGV
alignment
bwa-meth
updated 11 months ago by
Ram
41k • written 8.5 years ago by
mehran.karimzade
▴ 220
5
votes
7
replies
2.9k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 7 weeks ago by
Istvan Albert
99k • written 5.5 years ago by
chris.bird
▴ 10
5
votes
1
reply
403
views
Enricher with Gene Symbols
DGE
ClusterProfiler
Enrich
ORA
updated 3 months ago by
bk11
★ 1.8k • written 3 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
3
replies
908
views
abyss-pe genome assembly
konnector
abyss-pe
updated 5 months ago by
Ram
41k • written 4.8 years ago by
Igor Lalin
• 0
5
votes
6
replies
3.2k
views
Can't access DAVID
DAVID
updated 11 months ago by
Ram
41k • written 8.4 years ago by
komal.rathi
★ 4.1k
5
votes
2
replies
248
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
7 days ago by
Rafael Soler
★ 1.2k
5
votes
4
replies
942
views
Converting Bam file to Fasta (Zipped)
bedtools
samtools
updated 5 months ago by
Ram
41k • written 13 months ago by
Eliveri
▴ 350
5
votes
6
replies
1.3k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2
R
RNA-Seq
updated 5 months ago by
Ram
41k • written 3.6 years ago by
Ranan Jyoti Sarma
▴ 90
5
votes
5
replies
510
views
Convert genomic files from known Gigabases(# of bases) to gigabytes
gigabases
gigabytes
genomics
updated 9 months ago by
GenoMax
136k • written 9 months ago by
datanerd
▴ 520
5
votes
1
reply
582
views
Learning Linux advance commands
grep
awk
linux
sed
updated 8 weeks ago by
Zhitian Wu
▴ 60 • written 13 months ago by
rheab1230
▴ 140
4
votes
2
replies
2.1k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end
alignment
next-gen
updated 5 months ago by
Ram
41k • written 10.9 years ago by
Kenneth Daily
▴ 50
4
votes
7
replies
3.3k
views
PLINK gxe not reading covariate file
covariate
plink
gxe
updated 11 months ago by
Ram
41k • written 8.5 years ago by
jennavive00
▴ 20
4
votes
4
replies
615
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 6 months ago by
Joe
21k • written 6 months ago by
antoine.fauchois92
▴ 20
4
votes
6
replies
2.1k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 6 months ago by
minakshiboruahassam
• 0 • written 15 months ago by
Plus
▴ 20
4
votes
4
replies
504
views
Feedback on mouse brain scRNA-seq quality control
mouse
brain
singe-cell
scRNAseq
quality-control
3 months ago by
nshenoy
▴ 50
4
votes
7
replies
772
views
exome and genome data
exome
vcf
genome
gene
gnomad
updated 11 months ago by
Ram
41k • written 11 months ago by
Eliza
▴ 30
4
votes
1
reply
1.1k
views
Batch effect correction methods (Seurat v3, Harmony, fastMNN, Liger)
integration
Batch
seurat
fastMNN
Harmony
9 months ago by
re_raz
▴ 60
4
votes
2
replies
1.0k
views
Convert BAM files to GENOMEDATA files
BAM
genomedata
updated 8 months ago by
Ram
41k • written 5.6 years ago by
Armand
• 0
4
votes
3
replies
709
views
Testing overlap significance of three gene sets using the hypergeometric distribution
Hypergeometric-distribution
gene-sets
7 months ago by
Pac314
▴ 10
4
votes
8
replies
2.2k
views
6 follow
building snpEff database
snpEff
updated 9 months ago by
Ram
41k • written 19 months ago by
aabhordia
▴ 30
4
votes
11
replies
3.0k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 10 months ago by
Ram
41k • written 5.6 years ago by
mahdikhadem95
▴ 30
4
votes
2
replies
497
views
Analyzing bulk RNA-seq
RNAseq
updated 10 months ago by
swbarnes2
13k • written 10 months ago by
Zaid
• 0
4
votes
8
replies
2.1k
views
Select only sequences that align with X% of a query during blastp search
sequence
blast
alignment
updated 10 months ago by
Ram
41k • written 8.5 years ago by
dago
★ 2.8k
1,000 results • Page
3 of 20
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
Recent Locations •
All
Frankrike,
4 minutes ago
Tehran,
12 minutes ago
Singapore,
17 minutes ago
India,
22 minutes ago
Bologna,
23 minutes ago
China,
24 minutes ago
United States,
25 minutes ago
Recent Awards •
All
Popular Question
to
beausoleilmo
▴ 560
Commentator
to
Brian Bushnell
19k
Popular Question
to
Gama313
▴ 120
Popular Question
to
nanodano
▴ 30
Popular Question
to
shome
▴ 10
Popular Question
to
Malachi Griffith
19k
Scholar
to
jared.andrews07
★ 16k
Recent Replies
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
by
swbarnes2
13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
fluke
• 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts
by
Istvan Albert
99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
beausoleilmo
▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
CTLong
▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC
by
ayasu
• 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts
by
Brian Bushnell
19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
Brian Bushnell
19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters?
by
AMARU
• 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
Comment: "MethylKit" package for WGBS data
by
viveksomya123
• 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
Traffic: 790 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