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8
votes
15
replies
698
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How to convert plink files to Hapmap Format
GWAS Plink
updated 21 minutes ago by 141k • written 7 weeks ago by • 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 10 hours ago by ▴ 850 • written 6.1 years ago by ▴ 10
4
votes
2
replies
348
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 2 hours ago by • 0 • written 11 weeks ago by ▴ 20
4
votes
7
replies
400
views
To get p-values for the TPM
P-value TPM RSEM
updated 18 hours ago by ★ 5.8k • written 1 day ago by • 0
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 12 hours ago by • 0 • written 22 months ago by ▴ 180
3
votes
4
replies
200
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
7 hours ago by QX • 0
3
votes
8
replies
479
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 21 hours ago by 14k • written 1 day ago by ▴ 10
3
votes
3
replies
140
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 5 hours ago by 14k • written 11 hours ago by • 0
2
votes
4
replies
211
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
updated 6 hours ago by 43k • written 21 hours ago by ▴ 20
2
votes
1
reply
139
views
Finding orthologs between genome error
OMA OMAbrowser
updated 17 hours ago by ★ 1.1k • written 1 day ago by • 0
2
votes
3
replies
175
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
updated 15 hours ago by 161k • written 19 hours ago by ▴ 30
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 23 hours ago by • 0 • written 2.4 years ago by • 0
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 6 hours ago by 82k • written 3.9 years ago by ▴ 280
1
vote
1
reply
108
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign cell-markers
updated 6 hours ago by 43k • written 13 hours ago by ▴ 10
1
vote
2
replies
191
views
alignment result
RNA-seq samtools hisat2
21 hours ago by ahmad.sajad4541 • 0
1
vote
8
replies
747
views
Adding CB tag to bam file
samtools bam
updated 18 hours ago by 161k • written 7 days ago by • 0
1
vote
0
replies
61
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
10 hours ago by rohitsatyam102 ▴ 850
1
vote
2
replies
134
views
ScRNA data question
scRNA Vlnplot Samples
updated 9 hours ago by ▴ 10 • written 13 hours ago by ▴ 10
0
votes
1
reply
118
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment gaps
updated 19 hours ago by ▴ 170 • written 20 hours ago by • 0
0
votes
0
replies
48
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary correlation
10 hours ago by Emily ▴ 10
0
votes
0
replies
57
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
9 hours ago by avocado123 • 0
0
votes
1
reply
145
views
Network Alignment
plugin Cytoscape CytoMCS
updated 22 hours ago by ▴ 280 • written 1 day ago by ▴ 40
0
votes
2
replies
136
views
BLAST using both nucleotides and taxonomic local databases
blast ncbi taxid taxonomy
updated 8 hours ago by 141k • written 15 hours ago by ▴ 150
0
votes
1
reply
382
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 11 hours ago by • 0 • written 4 months ago by • 0
0
votes
1
reply
77
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 6 hours ago by 82k • written 7 hours ago by • 0
0
votes
1
reply
141
views
PCA plot
DESeq2 PCAplot
updated 12 hours ago by ▴ 170 • written 23 hours ago by ▴ 10
0
votes
5
replies
269
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 13 hours ago by 141k • written 1 day ago by ▴ 90
0
votes
0
replies
49
views
News: Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis Statistics R
updated 6 hours ago by 43k • written 10 hours ago by ★ 2.5k
0
votes
0
replies
67
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
17 hours ago by Aspire ▴ 300
0
votes
2
replies
145
views
Highest variable features in single cell data
single-cell
updated 6 hours ago by 43k • written 19 hours ago by • 0
0
votes
3
replies
277
views
Heatmap and rna-seq
RNA-Seq Heatmap
updated 6 hours ago by 43k • written 2 days ago by ▴ 10
0
votes
2
replies
186
views
Annovar using R package
Annovar gnomAD R
6 hours ago by DKA ▴ 40
0
votes
1
reply
134
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 6 hours ago by 43k • written 23 hours ago by ★ 3.9k
0
votes
0
replies
100
views
News: 8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq variant-calling RNA-seq illumina transcriptomics
updated 6 hours ago by 43k • written 1 day ago by 11k
0
votes
0
replies
44
views
Designing single-stable RNA molecules
structure RNA
5 hours ago by Edna • 0
0
votes
0
replies
51
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
5 hours ago by simplitia ▴ 130
0
votes
2
replies
173
views
why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
updated 5 hours ago by 43k • written 17 hours ago by ★ 1.8k
0
votes
4
replies
242
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
18 hours ago by sehriban.buyukkilic ▴ 10
0
votes
1
reply
65
views
Rare Disease Variant Pathway Analysis
Pathway analysis
updated 4 hours ago by 4.2k • written 4 hours ago by ▴ 10
0
votes
11
replies
438
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
3 hours ago by atowns21 • 0
0
votes
0
replies
50
views
how to read graph_test output of monocle 3
monocle3
10 hours ago by synat.keam ▴ 100
0
votes
0
replies
66
views
Job: CTO/founding engineer role at Voyant Bio
engineer
10 hours ago by Assaf • 0
42 results • Page 1 of 1
Recent Votes
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Answer: Missing protein (VEGF-A) in String db
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Recent Replies
Comment: Missing protein (VEGF-A) in String db by shalespringer • 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much, it actually worked!
Answer: Rare Disease Variant Pathway Analysis by LauferVA 4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification by swbarnes2 14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
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