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0
votes
2
replies
25
views
Problem with viewing BAM files in IGV
IGV BAM
just now by manfi • 0
0
votes
1
reply
23
views
TPM value from DESE2 and significant filterig isssue
DESE2 TPM value from
updated 1 hour ago by 53k • written 1 hour ago by • 0
0
votes
1
reply
53
views
Doing multiple testing correction before or after GO analysis
RNA-Seq testing comparison Statistics Multiple
updated 28 minutes ago by 53k • written 2 hours ago by • 0
0
votes
0
replies
55
views
Search predicted peptides from proteomes
peptide proteome search
4 hours ago by tomas4482 ▴ 40
0
votes
0
replies
63
views
Identification of cell types/groups in single-cell data
cell single type clustering
updated 3 hours ago by 33k • written 4 hours ago by ▴ 10
0
votes
0
replies
57
views
Are there some methods can be used to do association analysis in a very small size group?
gwas WGS study association
4 hours ago by Jackie • 0
1
vote
4
replies
166
views
TCGA dataset normalization
machine TCGA DESeq2 learning normalization
1 hour ago by ruby4bioinfo • 0
0
votes
0
replies
62
views
Plink --merge-list only outputting fam
plink bash
6 hours ago by J • 0
0
votes
0
replies
59
views
PRSice for validation in new sample set
Validation
7 hours ago by aredha2 ▴ 10
0
votes
0
replies
66
views
Proper way(s) to perform enrichment analysis in R
GSEA analysis enrichment R RNAseq
9 hours ago by cwwong13 • 0
0
votes
0
replies
40
views
Problem with Risk table in Kaplan-Meier plot
Kaplan-Meier ggplot2 Survival
10 hours ago by roberto.sb.93 • 0
1
vote
0
replies
38
views
Does civic api provide access to 'Flagging Comment'
civic
11 hours ago by Puru ▴ 10
0
votes
0
replies
35
views
how to identiify real isomers in mirge3.0's output files.
isomirs mirge3.0
11 hours ago by RNAseqer ▴ 160
0
votes
1
reply
50
views
RIP-seq : normalize Input with Immunoprecipitated raw counts or not
limma edgeR analysis RIP-seq RNA-seq DE table count Raw normalization
updated 22 minutes ago by 53k • written 11 hours ago by • 0
0
votes
0
replies
36
views
Clustal Omega on uniprot
comparing similarity alignments between two clustal Omega
11 hours ago by kodo64 • 0
0
votes
0
replies
49
views
Which files from PacBio output files to use in downstream analysis in R
analysis files output R PacBio
13 hours ago by eimanpharmacist ▴ 10
0
votes
1
reply
53
views
Quick questions about Alevin and AlevinQC
alevinqc alevin
updated 26 minutes ago by 53k • written 13 hours ago by ▴ 350
0
votes
1
reply
77
views
error related to module
conda python h5py module
updated 12 hours ago by 34k • written 13 hours ago by ▴ 20
0
votes
0
replies
31
views
Tools for the reconstruction of demographic history from genome sequences FOR POLYPLOIDS
MSMC SMC demographics genome polyploids
14 hours ago by poecile.pal ▴ 10
0
votes
0
replies
37
views
P-values far too high for quantitative regenie phenotype
regenie GWAS
14 hours ago by Dan • 0
0
votes
1
reply
91
views
WGCNA, what does it mean if no hub genes are identified?
WGCNA
updated 3 hours ago by ★ 1.7k • written 14 hours ago by ▴ 210
0
votes
3
replies
80
views
Changing the sample IDs of a bed/bim/fam PLINK fileset
plink
16 hours ago by Arta • 0
0
votes
1
reply
88
views
R genome reference library from cellranger-arc alignment
10Xgenomics cellranger-arc multiome signac
updated 15 hours ago by 53k • written 17 hours ago by ▴ 20
0
votes
0
replies
51
views
Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs
convert SNPs ID rsID
17 hours ago by pmw • 0
0
votes
0
replies
39
views
Seurat Integration Input Question
seurat integration
18 hours ago by ssontha2 • 0
0
votes
1
reply
83
views
Poly A vs total RNA - Which is better for extracting noncoding RNA information
noncodingRNA extractedmol scrnaseq
18 hours ago by swanti ▴ 10
1
vote
0
replies
44
views
How can we compare EdgeR to limma-voom?
limma-voom EdgeR
18 hours ago by Barista ▴ 10
0
votes
0
replies
30
views
Add additional masks to BSgenome without BSgenomeForge
masking hg38 BSgenome R
18 hours ago by monovich • 0
0
votes
0
replies
34
views
Regarding cellranger count and aggr functions
cellranger single-cell scrna-seq
19 hours ago by botloggy • 0
0
votes
1
reply
63
views
How to calculate phred score of fastq files?
linux phred fastq
updated 19 hours ago by 106k • written 19 hours ago by ▴ 60
0
votes
1
reply
50
views
command for isolate unique reads with unique subject id
blast
updated 20 hours ago by 53k • written 20 hours ago by ▴ 20
0
votes
0
replies
38
views
What is the codification in genestrand 1 and 2?
chipseeker peakannotation
1 day ago by Lila M ★ 1.1k
0
votes
0
replies
29
views
MGEs analysis in metagenomic data by ACLAME data base
MGE ACLAME
1 day ago by adnan.sabar7865 • 0
0
votes
0
replies
47
views
vcf to bgen conversion using qctool v2 yields 0 snps
bgen vcf qctool
updated 1 day ago by 12k • written 1 day ago by ▴ 50
0
votes
0
replies
50
views
Does anyone know how to install RING 2.0 on a linux machine from tar file.
RIN 2.0 RING PDB
1 day ago by Anjali • 0
0
votes
3
replies
143
views
bedtools getfasta concatenating sequences
bedtools getfasta
updated 48 minutes ago by ★ 6.3k • written 1 day ago by ▴ 30
0
votes
2
replies
112
views
BLAST versus HMM search
python coding programming putty
updated 1 day ago by 12k • written 1 day ago by • 0
0
votes
4
replies
134
views
Homer finds same peak multiple times
rnaseq peaks homer counts
updated 1 day ago by 53k • written 1 day ago by ▴ 10
4
votes
5
replies
179
views
Unable to download fastq files in parallel / SOS
slurm rna-seq bioinformatics fastq sequencing
updated 1 day ago by 49k • written 1 day ago by • 0
0
votes
0
replies
35
views
Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark
methylation
1 day ago by pixie@bioinfo ★ 1.4k
0
votes
0
replies
46
views
Correcting for leukocyt count in QuantSeq analysis
QuantSeq
1 day ago by Barista ▴ 10
0
votes
1
reply
74
views
Filter criteria for variants based on GBS data
gbs filter
updated 1 day ago by ★ 2.0k • written 1 day ago by ★ 4.9k
0
votes
0
replies
45
views
PPI-Network igraph for tissue-specific data
interaction protein igraph R network
1 day ago by bi.nb21 • 0
0
votes
0
replies
68
views
Use grep to loop a command in a script
snps grep vcftools script bash
updated 1 day ago by 106k • written 1 day ago by • 0
0
votes
0
replies
43
views
merge bfiles with different allele format by plink
plink merge bfile SNP
1 day ago by khn ▴ 130
0
votes
0
replies
40
views
How to find the effect of mutation in a sanger sequence using PolyPhen-2 ?
mutation-analysis sanger-sequencing
1 day ago by Babita Pruseth • 0
0
votes
1
reply
96
views
Problem about the uses of linkers
Linkers
updated 1 day ago by 5.8k • written 1 day ago by • 0
0
votes
0
replies
46
views
How to find adapter dimer present in a library from reads?
Library adapter_dimer tools reads
2 days ago by eli_bayat ▴ 50
0
votes
5
replies
170
views
How to extract protein sequences from published paper
DOI supplementary extract protein
updated 1 day ago by 106k • written 2 days ago by • 0
0
votes
0
replies
97
views
Compare gene expression between scRNAseq and bulk RNAseq data
scRNAseq RNAseq
2 days ago by grayapply2009 ▴ 240
1,000 results • Page 1 of 20
Recent Votes
Comment: TCGA dataset normalization
Understanding Imputed Genotypes
C: Cox regression survival analysis - using a panel of genes with TCGA
C: Scaling data using Pheatmap
C: Scaling data using Pheatmap
A: Database of HERV integration locations
A: Database of HERV integration locations
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Recent Replies
Comment: Beagle 5.2 Imputation Issue, understanding output by Matt • 0
The problem is with singleton sites (note the number of markers in your window). The solution is to exclude these scaffolds using the exclu…
Comment: Problem with viewing BAM files in IGV by manfi • 0
Samtools view: ![enter image description here][1] Screenshot for 1 line (I tried several, no data displayed): ![enter image description…
Comment: RIP-seq : normalize Input with Immunoprecipitated raw counts or not by ATpoint 53k
I have no experience with RIP-seq but usually in something like ChIP-seq one only uses inputs for peak calling as they are globally differe…
Comment: Quick questions about Alevin and AlevinQC by ATpoint 53k
> When I run AlevinQC why the Number of used reads (which Alevin documentation says are reads that are used for quantification) greater tha…
Comment: Problem with viewing BAM files in IGV by Pierre Lindenbaum 138k
> as verified by inspecting the BAM file with samtools view show us a few lines of "samtools view" and show us the screenshot of IGV for …
Answer: compare two vcf files by 순연 • 0
thank u sir , happy Korean Thanksgiving Day 1) how you want to rank those common rs IDs 선생님이 알려주신 코드를 이용해서 두개의 파일에 중복되는 rsID가 있고 또한 여…
Comment: Doing multiple testing correction before or after GO analysis by dsull ★ 2.3k
Honestly speaking, your gene list is not "statistically robust" (it's arbitrary since you have no sense of the actual false discovery rate)…
Comment: bedtools getfasta concatenating sequences by Juke34 ★ 6.3k
Ok it is because the first command create gene features only and the second remove gene feature if they do not have any sub-feature like mR…
Comment: What does it mean BLASTx in de novo RNAseq analysis? by lieven.sterck 12k
yes, that is very possible indeed. however, running blastx on the 'raw' genomic is somewhat less intuitive to interpret. If you have annot…
Comment: TPM value from DESE2 and significant filterig isssue by ATpoint 53k
Hi, could you please reformat this post using the code `10101` option to highlight code and data?
Comment: desEQ2 eRROR by Nai • 0
res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2Fo…
Comment: TCGA dataset normalization by ruby4bioinfo • 0
Thanks Kevin, i got following output str(countData) 'data.frame': 60488 obs. of 183 variables: $ Ensembl_ID : chr "ENSG00000000003…
Comment: Why there are same name with different value in my microarray result? by Aki • 0
Thank you JC! Do you know how to combine these spots as one miRNA? Or do we treat them differently?
Comment: What does it mean BLASTx in de novo RNAseq analysis? by Riku ▴ 40
Thank you very much for your advices! I see. It's an indicator of the quality of the assembly. Can this be done by running BLAST on the f…
Comment: DE analysis using technical replicates by vineshkamble23 • 0
Okay Thank you so much for the explanation
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