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17 results • Page
1 of 1
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Votes
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3
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389
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Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 23 hours ago by
yhdist
▴ 70 • written 3 days ago by
Cookin
• 0
2
votes
4
replies
234
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 22 hours ago by
Ram
40k • written 1 day ago by
P
• 0
1
vote
3
replies
178
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 19 hours ago by
Ram
40k • written 21 hours ago by
txema.heredia
▴ 80
1
vote
6
replies
209
views
STAR index not working
STAR
RNA-Seq
updated 19 hours ago by
Ram
40k • written 20 hours ago by
camillab.
▴ 130
1
vote
3
replies
165
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 23 hours ago by
GenoMax
134k • written 1 day ago by
anika.john
• 0
0
votes
10
replies
309
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
21 hours ago by
Y
• 0
0
votes
11
replies
650
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
19 hours ago by
evmae
• 0
0
votes
0
replies
77
views
Chromosome bias on RNA-Seq differential gene expression analysis
bias
rna-seq
chromosome
17 hours ago by
blz
▴ 10
0
votes
1
reply
101
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
entrez
esearch
biopython
efetch
epost
updated 17 hours ago by
GenoMax
134k • written 17 hours ago by
Salem
• 0
0
votes
2
replies
128
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 13 hours ago by
swbarnes2
13k • written 21 hours ago by
Mo
• 0
0
votes
4
replies
252
views
manhattan plot with vcf information
R
manhattan
vcf
9 hours ago by
sooni
▴ 10
0
votes
1
reply
52
views
Stuck at Conda version 23.1.0
23.1.0
update
conda
updated 56 minutes ago by
rpolicastro
12k • written 3 hours ago by
A_heath
▴ 140
0
votes
0
replies
6
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
4 minutes ago by
juliviglino
• 0
0
votes
0
replies
75
views
Any way to predict hormone biosynthesis pathways in understudied organisms?
genomics
orthologs
biosynthesis-pathway
updated 22 hours ago by
Ram
40k • written 1 day ago by
Mark
• 0
0
votes
0
replies
83
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
updated 22 hours ago by
Ram
40k • written 1 day ago by
Thomas
• 0
0
votes
1
reply
92
views
Prank checkpoint and restore?
prank
alignment
updated 21 hours ago by
Ram
40k • written 22 hours ago by
Pit
• 0
0
votes
2
replies
187
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
21 hours ago by
JLee
• 0
17 results • Page
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Answer: Bedtools - converting multiple bam files to bed
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Comment: Stuck at Conda version 23.1.0
by
rpolicastro
12k
Have you installed any software into your base environment?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
petebio
▴ 70
This might not necessarily be the best way to do an RNA-Seq analysis. RNA-Seq is famously sensitive to all sorts of factors like who did th…
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
Asaf
10k
Yes, you are correct. However, there are several things you should consider: 1. For DESeq2 to be able to normalize both datasets togeth…
Comment: Uniprot Database for download
by
Elisabeth Gasteiger
★ 2.3k
> This is the entry for your example accession: https://www.uniprot.org/uniprotkb?query=proteome%3AUP000005640+AND+C9J7I0 I would recommen…
Answer: Identifying common DEGs among multiple datasets
by
Barry Digby
★ 1.2k
Return a vector of common DEGs ```R dataset1 <- read.csv("dataset1.csv", header=T) dataset2 <- read.csv("dataset2.csv", header=T) h…
Comment: Dealing with transcriptome sequences that are smaller than their respective gene
by
langziv
▴ 50
If it's difficult to tell from RNA-seq data, what other approaches I should use?
Comment: Dealing with transcriptome sequences that are smaller than their respective gene
by
langziv
▴ 50
I modified the question so that instead of genes the question refers to CDSs.
Comment: Dealing with transcriptome sequences that are smaller than their respective gene
by
langziv
▴ 50
Thanks. Is there an approach or a guideline to filter such sequences?
Answer: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Juke34
8.2k
There are tools to combine output from blast in tabulated format like in the example here [enter link description here][1](see functional …
Answer: Importance of Data Structures for Bioinformatics?
by
xiaoguang
▴ 120
Bioinformatics is a cross-disciplinary research subject and learning anything is a plus for future participation in related jobs. But right…
Answer: How to find positions with higher depth relative to their surroundings
by
xiaoguang
▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files?
by
xiaoguang
▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data
by
Diana
• 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings
by
d-cameron
★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
Answer: How to retrieve LoF and missense variants in WES data?
by
luffy
▴ 30
@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
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