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976 results • Page 2 of 20
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5
votes
15
replies
4.9k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq IGV mapping
updated 24 days ago by • 0 • written 4.8 years ago by ▴ 160
23
votes
11
replies
4.8k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf fasta homopolymer repeat
updated just now by 43k • written 4.9 years ago by 47k
4
votes
14
replies
4.7k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 19 days ago by 43k • written 22 months ago by ▴ 20
4
votes
7
replies
4.4k
views
snakemake output directory
snakemake ngs
updated 6 hours ago by • 0 • written 3.9 years ago by ▴ 200
2
votes
2
replies
4.4k
views
Variant calling for sanger reads
variant-calling sanger alignment variants
updated 21 days ago by 43k • written 7.7 years ago by ▴ 70
18
votes
20
replies
4.3k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 6 days ago by 43k • written 7.5 years ago by ▴ 80
12
votes
13
replies
4.3k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression RNA-Seq glm DESeq2
updated 6 days ago by 43k • written 6.2 years ago by ★ 1.6k
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics 10x
7 days ago by firestar ★ 1.6k
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 6 days ago by 43k • written 6.2 years ago by ▴ 90
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 6 days ago by 43k • written 5.0 years ago by ▴ 260
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 20 days ago by 43k • written 6.2 years ago by 87k
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 6 days ago by 43k • written 5.5 years ago by ▴ 100
1
vote
10
replies
3.8k
views
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 2 days ago by ▴ 300 • written 18 months ago by • 0
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 22 hours ago by 43k • written 4.0 years ago by ▴ 330
2
votes
4
replies
3.7k
views
Tutorial for analysing gpr files of microarray
GPR microarray
updated 25 days ago by ▴ 10 • written 5.5 years ago by ▴ 190
1
vote
3
replies
3.6k
views
MSF Data Analysis
MSF Proteomics Thermo Proteome Discoverer
updated 12 days ago by • 0 • written 4.4 years ago by ▴ 130
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 6 days ago by 43k • written 6.5 years ago by ★ 1.6k
4
votes
2
replies
3.5k
views
Genome annotation: convert gtf to gff3 file
gff3 gtf
updated 21 days ago by • 0 • written 17 months ago by ▴ 50
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 21 days ago by 43k • written 5.5 years ago by ▴ 110
8
votes
12
replies
3.4k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 13 days ago by • 0 • written 3.4 years ago by ▴ 40
7
votes
7
replies
3.4k
views
How to perform normalization when converting ATAC bam file to bigwig file using deeptools for IGV visualization
bamCoverage deeptools bigwig IGV ATAC
updated 25 days ago by • 0 • written 2.2 years ago by ▴ 40
2
votes
6
replies
3.4k
views
Base Quality of a reported variant in VCF
alignment FASTQ VCF next-gen Variant-Calling
updated 21 days ago by 43k • written 9.2 years ago by ▴ 50
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 5 days ago by 43k • written 6.7 years ago by ▴ 10
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression RNA-Seq
updated 6 days ago by 43k • written 7.8 years ago by • 0
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen cutadapt
updated 18 days ago by 43k • written 5.6 years ago by ▴ 20
0
votes
3
replies
3.0k
views
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
R next-gen-sequencing absolute
updated 18 days ago by 43k • written 6.7 years ago by • 0
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 6 days ago by 43k • written 6.5 years ago by ★ 1.6k
7
votes
3
replies
3.0k
views
ISCN annotation for SV/CN VCF files
SV
updated 8 days ago by 4.2k • written 7 months ago by ▴ 50
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 22 hours ago by 43k • written 3.8 years ago by ▴ 250
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 22 days ago by • 0 • written 6.5 years ago by • 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 6 days ago by 43k • written 6.4 years ago by ▴ 10
2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer MSA intron-exon
updated 10 days ago by • 0 • written 6.6 years ago by ▴ 630
3
votes
16
replies
2.6k
views
design matrix for dge
limma differential-gene-expression r
updated 6 days ago by 43k • written 7.9 years ago by ▴ 50
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 6 days ago by 43k • written 8.0 years ago by ▴ 80
2
votes
1
reply
2.5k
views
CRAM reference registry and the GRch38 reference genome
BAM Samtools GRCh38 CRAM Variant-Calling
updated 21 days ago by 43k • written 5.3 years ago by ▴ 30
1
vote
6
replies
2.5k
views
Variant calling from multiple sequencing runs for a single samples
variant-calling
updated 21 days ago by 43k • written 7.0 years ago by • 0
1
vote
3
replies
2.4k
views
How to remove variants with 3+ alleles present Plink1.9
HaplotypeCaller GATK Plink1.9 vcftools
updated 25 days ago by • 0 • written 2.2 years ago by ▴ 10
8
votes
6
replies
2.4k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 7 days ago by 43k • written 3.5 years ago by ▴ 240
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq Somatic-Mutation Variant-Calling
updated 21 days ago by 43k • written 6.1 years ago by ▴ 600
0
votes
1
reply
2.4k
views
Job: Full Stack Web Developer - Cambridge, UK
JavaScript Python Visualisation
written 8.4 years ago by ▴ 400
12
votes
14
replies
2.4k
views
8 follow
Forum: Recovering bam files after unknown deletion in the storage
photorec bam sequencing
written 4.8 years ago by ▴ 70
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 7 days ago by 43k • written 3.7 years ago by ▴ 20
1
vote
5
replies
2.3k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 5 days ago by 81k • written 5.0 years ago by ▴ 750
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma microarray differential-gene-expression
updated 6 days ago by 43k • written 6.1 years ago by ▴ 170
2
votes
5
replies
2.3k
views
DGE on transcriptomic data, focus on transcript sequences or in derivated ORFs?
differential-gene-expression RNA-Seq ORFs
updated 6 days ago by 43k • written 6.4 years ago by ▴ 90
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps blast indel Variant-Calling
updated 21 days ago by 43k • written 7.6 years ago by ▴ 70
0
votes
4
replies
2.2k
views
Remove Gaps from Multiple sequence alignment
python MSA
updated 14 days ago by 43k • written 2.5 years ago by • 0
11
votes
4
replies
2.2k
views
long read + salmon? (transcript abundance)
long-read salmon
updated 10 days ago by 43k • written 13 months ago by ▴ 50
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 6 days ago by 43k • written 4.5 years ago by ▴ 20
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 6 days ago by 43k • written 2.7 years ago by ▴ 170
976 results • Page 2 of 20
Recent Votes
Comment: Bioinformatics_where do i start
Comment: Can I compare kallisto counts from samples with different amount of reads?
Comment: RNAseq of primary tumor and metastases in two different organ
Comment: CombineGVCFs vs. MergeVcfs
Comment: Bioinformatics_where do i start
Answer: Bwa sampe - BGI
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
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Popular Question to rbronste ▴ 420
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Recent Replies
Comment: Bwa sampe - BGI by ATpoint 81k
Honestly, use bwa mem like everyone else and call it a day. bwa mem ref.fa X1.fq.gz X_2.fq.gz | samtools sort -o sorted.bam See the b…
Comment: Bwa sampe - BGI by lorena9132 • 0
Hello, thank you very much for your response. I was referring more to using these options: -a INT Maximum insert size for a read pair …
Comment: gene body coverage with RSeqQC by BioinfGuru ★ 1.6k
Take a look at [this post][1] ... it might give a clue. Alternatively, for my installation the qcmodule is located at: /home/bioinfguru/…
Comment: Bioinformatics_where do i start by BioinfGuru ★ 1.6k
The [biostars handbook][1] is well worth the money [1]: https://www.biostarhandbook.com/
Comment: Statistical Advice Needed for RNAseq Data Analysis by David • 0
Thank you @atpoint for your reply, but I think I didn't explain myself clearly. Initially, I compared my two datasets to their control and …
Comment: RNAseq of primary tumor and metastases in two different organ by BioinfGuru ★ 1.6k
Most advise to avoid For Loops in R (don't ask me why, unexpected results and behaviours, poor efficiency I think). I would use tidyverse f…
Comment: RNAseq of primary tumor and metastases in two different organ by BioinfGuru ★ 1.6k
P-values are not corrected for the multiple comparisons inherent in differential gene expression analysis. FDR (aka qvalue) is used for sel…
Comment: CombineGVCFs vs. MergeVcfs by Jeremy Leipzig 22k
in the supplemental materials of that UKBB paper they actually do mention MergeVcfs but it must be a typo
Comment: add INFO tag to vcf with bcftools by Javier • 0
Hi, I'm trying to do something similar, could you share the code to do what you describe. Thanks
Comment: Visualization of PROKKA Annotation Result? by Joe 21k
Colin's answer is essentially the right one I believe, but the more immediate consideration is: *what are you actually trying to show?* Mo…
Comment: Bioinformatics_where do i start by Pierre Lindenbaum 161k
https://www.biostars.org/p/9554614/ ; <br> https://www.biostars.org/p/98983 ; <br> https://www.biostars.org/p/9583727/ :<br> https://www.b…
Answer: Bwa sampe - BGI by Pierre Lindenbaum 161k
bwa sampe produces unsorted SAM , not BAM. converting SAM to BAM will reduce the size sorting the BAM will reduce the size (you can …
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Bikram Kumar • 0
Hi! Should I delete the stack exchange post? I didn't know that cross posting is bad. [https://meta.stackoverflow.com/a/425789/5140632][1] …
Answer: Visualization of PROKKA Annotation Result? by colindaven 6.3k
You need a genome browser and you can probably use GBK or gff3 format. Here are some suggestions - I like JBrowse best, Artemis in its …
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Pierre Lindenbaum 161k
cross-posted https://bioinformatics.stackexchange.com/questions/22401
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