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116,754 results • Page
1 of 2336
Sort: Rank
Rank
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Votes
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0
votes
0
replies
1
view
creating batch colum for batch correction
batch
correction
combat
just now by
Expert
▴ 10
0
votes
2
replies
87
views
Segmentation error while using a tool
smalt
updated 20 minutes ago by
Mensur Dlakic
★ 27k • written 6 hours ago by
Ruqaiya
• 0
0
votes
0
replies
9
views
Help with DGEList function
bioinformatics
40 minutes ago by
Natali
• 0
0
votes
0
replies
13
views
Homer motif analysis
Homer
1 hour ago by
daffodil
▴ 10
0
votes
1
reply
70
views
HCL database download
database
HCL
human
updated 7 hours ago by
GenoMax
142k • written 8 hours ago by
sooni
▴ 20
0
votes
1
reply
93
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 5 hours ago by
Ram
43k • written 13 hours ago by
SHN
▴ 40
1
vote
1
reply
965
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
updated 9 hours ago by
lcordeiro
▴ 40 • written 14 months ago by
Zhenyu Zhang
★ 1.2k
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
181
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 10 hours ago by
chrchang523
10k • written 4 days ago by
8armed
• 0
0
votes
5
replies
231
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 10 hours ago by
chrchang523
10k • written 19 hours ago by
curious
▴ 750
0
votes
0
replies
65
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 4 hours ago by
Ram
43k • written 13 hours ago by
deepak180001
• 0
0
votes
1
reply
104
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 13 hours ago by
bk11
★ 2.4k • written 15 hours ago by
Rob
▴ 170
0
votes
1
reply
93
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 7 hours ago by
GenoMax
142k • written 14 hours ago by
Ximena
• 0
0
votes
1
reply
88
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 4 hours ago by
Ram
43k • written 14 hours ago by
Valentina
• 0
0
votes
6
replies
291
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 14 hours ago by
swbarnes2
14k • written 21 hours ago by
Erina
• 0
0
votes
1
reply
96
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 15 hours ago by
swbarnes2
14k • written 15 hours ago by
kalavattam
▴ 190
0
votes
1
reply
95
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 17 hours ago by
GenoMax
142k • written 17 hours ago by
Lada
▴ 30
0
votes
0
replies
72
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
18 hours ago by
Emilie
• 0
0
votes
0
replies
68
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
18 hours ago by
Javier
• 0
0
votes
1
reply
87
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 4 hours ago by
Thanujay S
• 0 • written 19 hours ago by
yahn
• 0
0
votes
0
replies
65
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
19 hours ago by
mikemakaveli1
• 0
0
votes
0
replies
68
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 19 hours ago by
Ram
43k • written 19 hours ago by
M.
▴ 30
0
votes
2
replies
127
views
Raw counts using stringtie
stringtie
RNA-seq
updated 19 hours ago by
GenoMax
142k • written 21 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
63
views
Modify plot R mtDNA indel
plot
mtDNA
R
21 hours ago by
marco.barr
▴ 90
0
votes
0
replies
102
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
21 hours ago by
NorbertK
• 0
2
votes
2
replies
147
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 21 hours ago by
t.montserrat.ayuso
▴ 10 • written 1 day ago by
carolofharvest
▴ 30
9
votes
9
replies
472
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 19 hours ago by
dsull
★ 6.0k • written 5 days ago by
carolofharvest
▴ 30
0
votes
2
replies
142
views
Downloading older version of a tool
Alignment
tools
6 hours ago by
Ruqaiya
• 0
0
votes
0
replies
79
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
23 hours ago by
rustykb
▴ 20
1
vote
1
reply
105
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 1 day ago by
ATpoint
82k • written 1 day ago by
adi.gershon1
• 0
3
votes
5
replies
199
views
Generating mpileup file using samtools
mpileup
samtools
updated 22 hours ago by
Joe
21k • written 1 day ago by
Ruqaiya
• 0
0
votes
5
replies
259
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 1 day ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
JH
• 0
1
vote
3
replies
214
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Qi
• 0
0
votes
0
replies
79
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
1 day ago by
Amos Bairoch
▴ 120
2
votes
3
replies
199
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 19 hours ago by
dthorbur
★ 1.9k • written 1 day ago by
Vijith
▴ 30
0
votes
0
replies
96
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
1 day ago by
Jeyong
• 0
0
votes
2
replies
682
views
homer not configured properly
Homer
makeTagDirectory
updated 1 day ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
200
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 1 day ago by
Alex Reynolds
35k • written 1 day ago by
SJP
• 0
0
votes
0
replies
92
views
Empty table plot using plotGseaTable()
FGSEA
14 hours ago by
Chris
▴ 260
0
votes
1
reply
138
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 1 day ago by
anovak
▴ 120 • written 1 day ago by
Hang
• 0
1
vote
3
replies
186
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
yvonneh
▴ 10
3
votes
5
replies
253
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
17 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 1 day ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
150
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
1
reply
177
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 1 day ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
1
vote
2
replies
202
views
RNA-seq data for deep learning classification
rna-seq
23 hours ago by
yahn
• 0
2
votes
6
replies
307
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 day ago by
Qroid
▴ 40
0
votes
1
reply
495
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 1 day ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
137
views
Provean help
variant
Provean
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Arun Sai Kumar
• 0
1
vote
1
reply
151
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Jeol
▴ 20
116,754 results • Page
1 of 2336
Recent Votes
Answer: Searching for gene in multiple genomes
Comment: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
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Recent Replies
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. If going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon.
by
lcordeiro
▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
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