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9
votes
7
replies
5.4k
views
How to combine a different sources of pathway database (KEGG, BioCarta) for Pathway analysis.
Pathway enrichment analysis GWAS pathway analysis
7.9 years ago by kmsh410 ▴ 40
9
votes
10
replies
2.8k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK Whole Exome Sequencing Mutect2
3.3 years ago by kwanghoon ▴ 20
9
votes
5
replies
3.9k
views
What's the interpretation behind Pathway enrichment analysis
networks pathway enrichment analysis gene
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 260
9
votes
12
replies
1.5k
views
Copy number variations analysis
R CNV
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 70
9
votes
4
replies
5.6k
views
How to analyse normalized read count?
RNA-Seq R
updated 16 months ago by 43k • written 9.0 years ago by ▴ 150
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R gene sequence SNP
5.5 years ago by bioinfo456 ▴ 150
9
votes
19
replies
2.4k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.3 years ago by schlogl ▴ 160
9
votes
6
replies
1.9k
views
Question about featureCounts
RNA-Seq featurecounts
updated 2.8 years ago by • 0 • written 4.6 years ago by ▴ 30
9
votes
20
replies
4.3k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard SAM
updated 14 months ago by 43k • written 5.8 years ago by ▴ 710
9
votes
4
replies
1.7k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
updated 13 months ago by 43k • written 7.8 years ago by ▴ 60
9
votes
6
replies
1.4k
views
Genotype meaning
genotype BL21
2.8 years ago by A_heath ▴ 160
9
votes
9
replies
4.7k
views
ATAC-seq TSS profile plot interpretation
ATAC-seq TSS V-plot
4.5 years ago by nanoide ▴ 120
9
votes
7
replies
5.6k
views
fisher test with multiple samples
statistics
updated 2.5 years ago by 43k • written 9.8 years ago by ▴ 220
9
votes
3
replies
7.2k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics rna
updated 5.2 years ago by 20 • written 12.1 years ago by ▴ 380
9
votes
13
replies
2.5k
views
Reannotating a gene: Identifying translation and transcription start sites
RNA-Seq genome gene
7.4 years ago by rh5118 ▴ 40
9
votes
2
replies
593
views
Answer needed urgently
Deep
updated 20 months ago by ★ 27k • written 20 months ago by • 0
9
votes
11
replies
1.5k
views
6 follow
Split up excel cell into multiple records
excel byonic
6.8 years ago by rshipman ▴ 30
9
votes
5
replies
3.8k
views
Which bias flags to run with Salmon before DESeq2 analysis?
RNA-Seq Salmon DESeq2 Bias Flags
4.9 years ago by cameron.holman ▴ 20
9
votes
11
replies
4.5k
views
please someone help me with running mirdeep2
software error mirdeep2 perl
7.6 years ago by zizigolu ★ 4.3k
9
votes
13
replies
2.0k
views
Archeological DNA sample - how to analyze
unmapped paleogenomics archeogenomics Assembly
2.3 years ago by Aruna ▴ 30
9
votes
14
replies
4.4k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 70
9
votes
7
replies
2.8k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression differential average R rna-seq
updated 2.8 years ago by ▴ 60 • written 2.9 years ago by ▴ 250
9
votes
7
replies
3.8k
views
7 follow
Are 2 replicates per sample sufficient for RNA-seq data analysis?
RNA-Seq R Ngs
6.2 years ago by Arindam Ghosh ▴ 510
9
votes
13
replies
15k
views
GC Content of Fasta file --- Python Help
sequence
7.2 years ago by Patrick Brennan ▴ 50
9
votes
4
replies
2.1k
views
[Code] Converte fasta/fa files to fastq
perl fastq sed fasta
updated 21 months ago by 43k • written 8.5 years ago by ★ 9.4k
9
votes
8
replies
1.7k
views
Union of unaligned fastq reads
RNA-Seq
6.9 years ago by Jeffin Rockey ★ 1.3k
8
votes
14
replies
2.4k
views
6 follow
Definition of "=" in comparing two genes
sequencing gene
updated 2.5 years ago by 43k • written 9.9 years ago by • 0
8
votes
6
replies
1.2k
views
I have 2 identical jupyter notebooks and I get BiomartException when I run one but not the other.
biomart python
updated 4.3 years ago by 20 • written 4.3 years ago by ▴ 50
8
votes
8
replies
1.6k
views
Clustering DNA sequences (from human genome)
sequencing genome
4.7 years ago by abdul.karim • 0
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
6.3 years ago by Sharon ▴ 610
8
votes
1
reply
8.6k
views
Correlation heatmaps: use correlation as clustering distance or not?
heatmap RNA-Seq clustering
5.1 years ago by CuriousGuy ▴ 90
8
votes
5
replies
851
views
Frustrated with DEA results
microarray differential-expression
updated 7 months ago by ★ 6.0k • written 7 months ago by • 0
8
votes
8
replies
1.8k
views
6 follow
DESeq2 adjusted p-values of 0 when p-value > 0.05
RNA-seq DEseq2
updated 3.0 years ago by ▴ 390 • written 3.0 years ago by • 0
8
votes
6
replies
2.3k
views
Using Bandage to finish ambiguous long-read assembly?
Assembly Bandage long reads Unicycler
updated 5.3 years ago by 20 • written 5.4 years ago by ★ 2.0k
8
votes
20
replies
3.0k
views
Why does cufflinks split this transcript?
RNA-Seq cufflinks assembly
6.3 years ago by corend ▴ 70
8
votes
12
replies
4.3k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 14 months ago by 43k • written 2.8 years ago by ▴ 30
8
votes
9
replies
1.5k
views
6 follow
Featurecount is 0 while TPM is 6289.54
TPM Count Feature
2.4 years ago by zhangmeng21 ▴ 10
8
votes
8
replies
1.9k
views
Sequence alignment algorithm for big size genes in MATLAB
alignment Matlab next-gen
7.0 years ago by r.tor ▴ 50
8
votes
13
replies
2.5k
views
Issue about install Cutadapt in ubuntu1404
cutadapt
7.1 years ago by Joe ▴ 30
8
votes
4
replies
2.4k
views
Global Sequence Alignment
alignment
11.0 years ago by behrang • 0
8
votes
7
replies
5.9k
views
Download human 3 UTR FASTA file
genome
8.2 years ago by bharata1803 ▴ 560
8
votes
11
replies
3.6k
views
Semantic Similarity selection in REVIGO: which is better? many clusters or few?
go revigo gene ontology
6.5 years ago by Farbod ★ 3.4k
8
votes
5
replies
3.6k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM FASTQ
updated 17 months ago by 43k • written 8.9 years ago by ▴ 60
8
votes
7
replies
3.9k
views
6 follow
Compatibility between my reference genome and GTF file
rna-seq hisat2 alignment reference genome
5.6 years ago by Batu ▴ 250
8
votes
8
replies
1.5k
views
microRNA-seq sequence lenght distribution after trimming
alignment rna-seq
5.3 years ago by szabo.marton ▴ 10
8
votes
3
replies
1.2k
views
Package installation error using Bioconda
antismash Bioconda
17 months ago by A_heath ▴ 160
8
votes
10
replies
2.0k
views
FASTA of translated amino acid sequences in their six reading frames, which one is the optimal?
aminoacid protein peptide Reading optimal frames
2.8 years ago by Luis999 ▴ 20
8
votes
7
replies
596
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 3 months ago by 43k • written 3 months ago by ▴ 100
8
votes
25
replies
3.1k
views
construction of a database
sql noSQL neo4j database
updated 14 months ago by 43k • written 3.0 years ago by ▴ 20
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 4.5 years ago by • 0 • written 6.8 years ago by ▴ 140
1,000 results • Page 4 of 20
Recent Votes
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
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Recent Replies
Comment: Doubt about the process of annotation, detection, identification and classificat by MarcosCosta • 0
Thank you very much, you've helped me a lot
Comment: Filtering VCF files based on VAF giving incorrect results by Arton • 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R by Ghada • 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome by Zhenyu Zhang ★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R by marco.barr ▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome by shpak.max ▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Pierre Lindenbaum 161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome by Pierre Lindenbaum 161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline? by yura.grabovska ▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file by asalimih ▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R by Lélé ▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations by GenoMax 142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations by Pierre Lindenbaum 161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R by Ghada • 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
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