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Limit : this week
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186 results • Page
1 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
13
views
Segmentation error while using a tool
error
tools
1 hour ago by
Ruqaiya
• 0
0
votes
1
reply
35
views
HCL database download
database
HCL
human
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
sooni
▴ 20
0
votes
1
reply
73
views
Design matrix Differential expression analysis
expression
designmatrix
analysis
Differential
RNA-sequence
updated 3 hours ago by
Gordon Smyth
★ 7.1k • written 8 hours ago by
SHN
▴ 40
1
vote
1
reply
951
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
updated 4 hours ago by
lcordeiro
▴ 40 • written 14 months ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
164
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 5 hours ago by
chrchang523
10k • written 3 days ago by
8armed
• 0
0
votes
5
replies
207
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 5 hours ago by
chrchang523
10k • written 14 hours ago by
curious
▴ 750
0
votes
0
replies
48
views
Quetion regarding WGCNA
WGCNA
Network
construction
7 hours ago by
deepak180001
• 0
0
votes
1
reply
85
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 8 hours ago by
bk11
★ 2.4k • written 9 hours ago by
Rob
▴ 170
0
votes
1
reply
70
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 2 hours ago by
GenoMax
142k • written 9 hours ago by
Ximena
• 0
0
votes
1
reply
67
views
filtering before dada2
metagenomic
bbduk
qiime2
dada2
bioinformatics
updated 2 hours ago by
GenoMax
142k • written 9 hours ago by
Valentina
• 0
0
votes
6
replies
268
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 9 hours ago by
swbarnes2
14k • written 16 hours ago by
Erina
• 0
0
votes
1
reply
78
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 10 hours ago by
swbarnes2
14k • written 10 hours ago by
kalavattam
▴ 190
0
votes
1
reply
81
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 11 hours ago by
GenoMax
142k • written 12 hours ago by
Lada
▴ 30
0
votes
0
replies
63
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
13 hours ago by
Emilie
• 0
0
votes
0
replies
58
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
13 hours ago by
Javier
• 0
0
votes
0
replies
52
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
14 hours ago by
yahn
• 0
0
votes
0
replies
58
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
14 hours ago by
mikemakaveli1
• 0
0
votes
0
replies
61
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 14 hours ago by
Ram
43k • written 14 hours ago by
M.
▴ 30
0
votes
2
replies
116
views
Raw counts using stringtie
stringtie
RNA-seq
updated 13 hours ago by
GenoMax
142k • written 15 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
56
views
Modify plot R mtDNA indel
plot
mtDNA
R
16 hours ago by
marco.barr
▴ 90
0
votes
0
replies
76
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
16 hours ago by
NorbertK
• 0
2
votes
2
replies
137
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 16 hours ago by
t.montserrat.ayuso
▴ 10 • written 20 hours ago by
carolofharvest
▴ 30
9
votes
9
replies
462
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 14 hours ago by
dsull
★ 6.0k • written 4 days ago by
carolofharvest
▴ 30
0
votes
2
replies
112
views
Downloading older version of a tool
Alignment
tools
1 hour ago by
Ruqaiya
• 0
0
votes
0
replies
71
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
18 hours ago by
rustykb
▴ 20
1
vote
1
reply
95
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 20 hours ago by
ATpoint
82k • written 20 hours ago by
adi.gershon1
• 0
3
votes
5
replies
190
views
Generating mpileup file using samtools
mpileup
samtools
updated 17 hours ago by
Joe
21k • written 20 hours ago by
Ruqaiya
• 0
0
votes
5
replies
251
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 21 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
JH
• 0
1
vote
3
replies
206
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
Qi
• 0
0
votes
0
replies
72
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
23 hours ago by
Amos Bairoch
▴ 120
2
votes
3
replies
187
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 14 hours ago by
dthorbur
★ 1.9k • written 23 hours ago by
Vijith
▴ 30
0
votes
0
replies
88
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
1 day ago by
Jeyong
• 0
0
votes
2
replies
676
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
190
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
83
views
Empty table plot using plotGseaTable()
FGSEA
9 hours ago by
Chris
▴ 260
0
votes
1
reply
131
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
179
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
242
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
11 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
142
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
1
reply
171
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
194
views
RNA-seq data for deep learning classification
rna-seq
17 hours ago by
yahn
• 0
2
votes
6
replies
299
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
488
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
129
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
143
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
1
vote
1
reply
150
views
Super ehancers
enhancers
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
Oburah
• 0
0
votes
6
replies
263
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 15 hours ago by
dsull
★ 6.0k • written 1 day ago by
Chen
• 0
5
votes
5
replies
238
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 1 day ago by
atharvakarkare14
▴ 30 • written 1 day ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
422
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
18 hours ago by
eebloom
▴ 80
186 results • Page
1 of 4
Recent Votes
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?
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
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Recent Awards •
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Popular Question
to
SHN
▴ 40
Popular Question
to
Rob
▴ 170
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to
GenoMax
142k
Popular Question
to
curious
▴ 750
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▴ 30
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carolofharvest
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Recent Replies
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, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Mbofire
• 0
I need assistance don't know what to do next after signing up
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
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