Limit : this year
all time today this week this month this year
1,000 results • Page 1 of 20
Sort: Views
Rank Views Votes Replies
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 11 months ago by 43k • written 5.7 years ago by ▴ 30
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel R statistics
updated 11 months ago by 43k • written 5.2 years ago by ▴ 60
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 4 weeks ago by 43k • written 6.9 years ago by ★ 1.3k
0
votes
8
replies
10.0k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by 43k • written 6.8 years ago by • 0
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic rna-seq trinity
updated 8 months ago by 43k • written 8.0 years ago by ▴ 110
4
votes
12
replies
7.9k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 3 months ago by ▴ 10 • written 3.4 years ago by ▴ 60
2
votes
9
replies
7.7k
views
6 follow
Read MAP and PED files in PLINK
GWAS PLINK
updated 4 months ago by 142k • written 6.0 years ago by • 0
5
votes
5
replies
7.3k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 5 weeks ago by • 0 • written 3.8 years ago by ★ 1.8k
0
votes
7
replies
7.3k
views
Problem in in alignment by muscle
sequence muscle alignment
updated 10 months ago by 43k • written 6.8 years ago by ▴ 70
6
votes
4
replies
6.6k
views
What is gnomAD allele frequency
AF gnomAD
updated 4 months ago by ▴ 760 • written 3.1 years ago by ▴ 50
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 17 days ago by • 0 • written 5.1 years ago by 11k
3
votes
7
replies
6.4k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 11 months ago by ★ 4.3k • written 6.3 years ago by ▴ 980
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 10 months ago by 43k • written 8.1 years ago by ▴ 50
1
vote
3
replies
6.2k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID org.Dr.eg.db
updated 4 weeks ago by 43k • written 5.6 years ago by ▴ 170
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 4 weeks ago by 43k • written 7.7 years ago by ▴ 70
3
votes
14
replies
6.1k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn mbedtls blast linux blast+
updated 4 months ago by ▴ 40 • written 3.1 years ago by • 0
2
votes
14
replies
6.0k
views
Using sam-dump in SRA toolkit to download chr20.bam from NA12878
sratoolkit sam-dump
updated 10 months ago by 43k • written 7.1 years ago by ▴ 10
0
votes
5
replies
6.0k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 29 days ago by • 0 • written 6.5 years ago by ▴ 30
0
votes
4
replies
5.9k
views
using IGV to visualize RNA seq alignment to transcriptome
rna-seq igv alignment
updated 8 months ago by 43k • written 7.9 years ago by ▴ 110
1
vote
5
replies
5.8k
views
Generate VCF File from Bam file and fasta by GATK
vcf SNP genome next-gen
updated 10 months ago by 43k • written 6.8 years ago by ▴ 70
0
votes
3
replies
5.6k
views
Bedgraphtobigwig Conversion Difficulties
bigwig
updated 10 months ago by 43k • written 11.2 years ago by • 0
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq rna-seq htseq FPKM TPM
updated 9 months ago by 82k • written 5.1 years ago by ▴ 210
0
votes
1
reply
5.4k
views
Hapmap to vcf
vcf hapmap
updated 10 months ago by 43k • written 5.7 years ago by ▴ 150
0
votes
8
replies
5.4k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 5 weeks ago by • 0 • written 4.8 years ago by ▴ 180
2
votes
11
replies
5.3k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 4 months ago by ▴ 210 • written 7.8 years ago by ▴ 20
3
votes
4
replies
5.2k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 9 months ago by ▴ 10 • written 8.7 years ago by ★ 1.4k
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig read-length deeptools ATAC-seq
updated 11 months ago by 43k • written 4.3 years ago by ▴ 50
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 11 months ago by 43k • written 5.3 years ago by ▴ 80
1
vote
4
replies
4.8k
views
TCGA data(RPKM) differential gene expression
rna-seq R TCGA RPKM IPA
10 months ago by realnewbie ▴ 30
3
votes
2
replies
4.8k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 9 months ago by ▴ 30 • written 4.5 years ago by ▴ 180
2
votes
7
replies
4.7k
views
SRA toolkit internet settings
sratoolkit fastq-dump sequencing RNA-Seq
updated 10 months ago by 43k • written 7.8 years ago by ▴ 90
1
vote
9
replies
4.6k
views
Unable to install bioconda and bowtie
bioconda conda
updated 5 months ago by 13k • written 20 months ago by ▴ 40
7
votes
13
replies
4.5k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq trimming fastqc
updated 6 months ago by 82k • written 3.5 years ago by ▴ 10
0
votes
8
replies
4.5k
views
Downloading single cell data from NCBI
ncbi rna-seq fastq-dump single-cell
updated 8 months ago by 43k • written 5.4 years ago by ▴ 380
0
votes
7
replies
4.5k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq alignment software-error next-gen sequence
updated 5 months ago by 43k • written 6.0 years ago by • 0
1
vote
0
replies
4.4k
views
how to convert .geno/.snp/.ind to .bed/.bim/.fam (ped plink format) in Windows
plink genomes ancestrymap
updated 10 months ago by 43k • written 7.9 years ago by ▴ 10
3
votes
4
replies
4.4k
views
Atypical volcano plot RNA-seq
volcano-plot RNA-seq deseq2
updated 8 months ago by 43k • written 5.5 years ago by ▴ 20
11
votes
22
replies
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 5 weeks ago by 43k • written 5.1 years ago by ▴ 270
7
votes
8
replies
4.3k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 11 months ago by 43k • written 4.0 years ago by ▴ 60
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 4 weeks ago by 43k • written 7.7 years ago by ★ 1.2k
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 5 weeks ago by 43k • written 5.6 years ago by ▴ 100
1
vote
7
replies
4.1k
views
Adjust width of annotations in pheatmap
R heatmap
updated 7 months ago by 88k • written 5.5 years ago by ▴ 30
5
votes
19
replies
4.1k
views
8 follow
Hisat2 aligner problem
RNA-Seq ChIP-Seq alignment Assembly software error
updated 4 months ago by 82k • written 5.0 years ago by ▴ 340
2
votes
4
replies
4.0k
views
Transcriptomic Coordinate Bam To Genomic Coordinate Bam
bam genomics
updated 10 months ago by 43k • written 11.3 years ago by ▴ 80
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 days ago by • 0 • written 5.6 years ago by 8.5k
1
vote
5
replies
4.0k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis Time-series pairwise
updated 11 months ago by 43k • written 7.7 years ago by ▴ 470
1
vote
8
replies
3.9k
views
No gene can be mapped
R GSEA
updated 5 months ago by ★ 1.8k • written 2.4 years ago by ▴ 10
0
votes
16
replies
3.9k
views
Gff to genbank - feature is missing
DNA augustus gff3 genbank
updated 12 months ago by 43k • written 6.0 years ago by ▴ 10
0
votes
7
replies
3.8k
views
MUMmer plot visualization
MUMmer plot
updated 3 months ago by • 0 • written 3.3 years ago by ▴ 90
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 13 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
1,000 results • Page 1 of 20
Recent Votes
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Comment: Duplicated sequence samtools
Answer: Duplicated sequence samtools
Recent Locations • All
Australia, 2 minutes ago
India, 7 minutes ago
United States, 9 minutes ago
United States, 12 minutes ago
United States, 23 minutes ago
Poole, Dorset, 24 minutes ago
Cambridge, MA, 33 minutes ago
Recent Awards • All
Scholar to Pierre Lindenbaum 161k
Voter to Sara ▴ 30
Popular Question to carlopecoraro2 ★ 2.5k
Popular Question to scideas ▴ 30
Popular Question to Muhammad • 0
Popular Question to synat.keam ▴ 100
Scholar to jv ★ 1.8k
Recent Replies
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by KHURRAM SHAHZAD • 0
Thank you it works
Answer: Add stats to the plot by Ghada • 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot by GenoMax 142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files by Tommaso • 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot by Ghada • 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim() by ATpoint 82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis by LauferVA 4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2 by Ezequiel • 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Traffic: 1061 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6