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191 results • Page
2 of 4
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1
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3
replies
302
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How to assign cell types after integration in scRNA
scRNA-seq
updated 5 days ago by
ATpoint
82k • written 6 days ago by
Francesco
▴ 10
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
2 days ago by
eebloom
▴ 80
1
vote
1
reply
224
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 4 days ago by
Michael
54k • written 4 days ago by
Lissa Cruz Saavedra
• 0
1
vote
7
replies
503
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 5 days ago by
bk11
★ 2.4k • written 9 days ago by
starswillfade
▴ 10
1
vote
3
replies
194
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
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 1 day ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
2
replies
241
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
2 days ago by
rianna.collins
• 0
1
vote
3
replies
207
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 1 day ago by
Alex Reynolds
35k • written 1 day ago by
SJP
• 0
1
vote
2
replies
340
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
6 days ago by
Francesco
▴ 10
1
vote
2
replies
225
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
Ravita
• 0
1
vote
3
replies
221
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
1
vote
8
replies
467
views
Downsampling fastq file
downsample
fastq
3 days ago by
marco.barr
▴ 90
1
vote
5
replies
314
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
1 day ago by
Riccardo
▴ 10
1
vote
3
replies
219
views
Odd alignment question/finding
Alignment
updated 1 day ago by
barslmn
★ 2.1k • written 2 days ago by
poordumbsillyidiot
• 0
1
vote
1
reply
114
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 1 day ago by
ATpoint
82k • written 1 day ago by
adi.gershon1
• 0
1
vote
7
replies
423
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
1 day ago by
eebloom
▴ 80
1
vote
2
replies
277
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
1 day ago by
eebloom
▴ 80
1
vote
2
replies
208
views
RNA-seq data for deep learning classification
rna-seq
1 day ago by
yahn
• 0
1
vote
3
replies
385
views
PCA plot
DESeq2
PCAplot
updated 5 days ago by
LauferVA
4.2k • written 9 days ago by
Aaliya
▴ 10
1
vote
3
replies
274
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 3 days ago by
GenoMax
142k • written 4 days ago by
jeffrey.maurer.informatics
• 0
1
vote
0
replies
186
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
2 days ago by
carlopecoraro2
★ 2.5k
1
vote
1
reply
170
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
3 days ago by
heelpPlease
• 0
1
vote
1
reply
226
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 3 days ago by
Ram
43k • written 4 days ago by
Jonathan Yoou
▴ 60
1
vote
6
replies
328
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 1 day ago by
GenoMax
142k • written 19 days ago by
eebloom
▴ 80
1
vote
1
reply
132
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 90
1
vote
1
reply
144
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Ruqaiya
• 0
1
vote
3
replies
393
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 5 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
O.rka
▴ 710
1
vote
1
reply
155
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
Jeol
▴ 20
1
vote
2
replies
281
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
3 days ago by
Nafi
• 0
1
vote
7
replies
504
views
gvcf joint calling
WES
GATK
VCF
gVCF
6 days ago by
zihanss
• 0
0
votes
0
replies
86
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
1 day ago by
Amos Bairoch
▴ 120
0
votes
5
replies
291
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 1 day ago by
Mohamed Abderrahmane
▴ 20 • written 5 days ago by
matteo.levorato
• 0
0
votes
5
replies
267
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 2 days ago by
JH
• 0
0
votes
0
replies
86
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
1 day ago by
rustykb
▴ 20
0
votes
0
replies
133
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
1 day ago by
NorbertK
• 0
0
votes
0
replies
69
views
Modify plot R mtDNA indel
plot
mtDNA
R
1 day ago by
marco.barr
▴ 90
0
votes
6
replies
272
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 1 day ago by
dsull
★ 6.0k • written 2 days ago by
Chen
• 0
0
votes
0
replies
72
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
1 day ago by
mikemakaveli1
• 0
0
votes
0
replies
74
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
2
replies
134
views
Raw counts using stringtie
stringtie
RNA-seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
76
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
1 day ago by
Javier
• 0
0
votes
0
replies
78
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
23 hours ago by
Emilie
• 0
0
votes
1
reply
102
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
Lada
▴ 30
0
votes
1
reply
108
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 20 hours ago by
swbarnes2
14k • written 21 hours ago by
kalavattam
▴ 190
0
votes
6
replies
307
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 19 hours ago by
swbarnes2
14k • written 1 day ago by
Erina
• 0
0
votes
0
replies
98
views
Empty table plot using plotGseaTable()
FGSEA
19 hours ago by
Chris
▴ 260
0
votes
1
reply
115
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 18 hours ago by
bk11
★ 2.4k • written 20 hours ago by
Rob
▴ 170
0
votes
5
replies
244
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 16 hours ago by
chrchang523
10k • written 1 day ago by
curious
▴ 750
0
votes
1
reply
193
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 16 hours ago by
chrchang523
10k • written 4 days ago by
8armed
• 0
0
votes
1
reply
105
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 13 hours ago by
GenoMax
142k • written 20 hours ago by
Ximena
• 0
191 results • Page
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Comment: Design matrix Differential expression analysis
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Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
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I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
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82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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Ruqaiya
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This the tool still problematic?
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Ruqaiya
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Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
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Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
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by
Thanujay S
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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
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Thanujay S
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Hey! Can you explain the question further? What have you tried?
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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…
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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…
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142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
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by
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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…
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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…
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