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1,000 results • Page 1 of 20
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20
votes
17
replies
3.3k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by ★ 1.2k • written 3.3 years ago by ▴ 110
15
votes
16
replies
1.8k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by 142k • written 7 months ago by ★ 1.2k
14
votes
10
replies
969
views
How to remove center population from seurat cluster
single-cell
4 months ago by synat.keam ▴ 100
14
votes
18
replies
2.3k
views
Clustering in single cell
seurat single-cell
updated 6 months ago by ▴ 210 • written 7 months ago by ▴ 280
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 23 days ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 4 weeks ago by 43k • written 5.0 years ago by ▴ 270
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 4.2 years ago by ▴ 50
10
votes
6
replies
990
views
RNA seq, secreted protein
protein gene secreted
updated 9 months ago by 21k • written 17 months ago by ▴ 170
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
10 months ago by Chris ▴ 280
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 11 months ago by 43k • written 8.1 years ago by ▴ 330
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 10 months ago by 43k • written 5.6 years ago by ▴ 30
9
votes
5
replies
512
views
Annotation of Complex Heatmap
complexheatmap
3 months ago by abiuma ▴ 30
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
5 months ago by analyst ▴ 50
9
votes
5
replies
738
views
Prophage prediction tool
prophage PHASTER prediction
updated 9 months ago by 142k • written 9 months ago by ▴ 160
8
votes
10
replies
792
views
bash script
whole-genome-sequencing
updated 24 days ago by 43k • written 4 weeks ago by ▴ 30
8
votes
5
replies
2.0k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 7 months ago by 43k • written 2.6 years ago by ▴ 160
8
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
10 months ago by yoshifumimiya ▴ 40
8
votes
6
replies
944
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari structural-variants r vcf venn-diagram
6 months ago by Matteo Ungaro ▴ 100
8
votes
7
replies
589
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 12 weeks ago by 43k • written 3 months ago by ▴ 100
8
votes
5
replies
844
views
Frustrated with DEA results
microarray differential-expression
updated 7 months ago by ★ 6.0k • written 7 months ago by • 0
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
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
7
votes
13
replies
985
views
deal with PCA and my samples
PCA DEG meta-analysis
6 months ago by ali • 0
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
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 11 months ago by 43k • written 4.0 years ago by ▴ 60
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.8 years ago by ▴ 40
7
votes
6
replies
1.4k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 11 months ago by 82k • written 11 months ago by ▴ 190
7
votes
9
replies
1.2k
views
Calculation of TMB on gene level
genomics
updated 7 months ago by ▴ 680 • written 7 months ago by ▴ 20
7
votes
3
replies
1.6k
views
What are the best tools for Genome assembly
Assembly genome
updated 11 months ago by 43k • written 5.8 years ago by ▴ 10
7
votes
12
replies
1.7k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome bwa bash
updated 6 months ago by 43k • written 4.2 years ago by ▴ 310
7
votes
7
replies
612
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
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
6
votes
3
replies
2.0k
views
Gene network with expression data
network RNA-Seq
updated 10 months ago by 43k • written 6.5 years ago by ▴ 30
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.1 years ago by ▴ 70
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 12 months ago by 43k • written 15 months ago by ▴ 50
6
votes
5
replies
778
views
merging replicates
ChIP-seq
updated 4 months ago by 82k • written 4 months ago by • 0
6
votes
4
replies
6.6k
views
What is gnomAD allele frequency
AF gnomAD
updated 3 months ago by ▴ 760 • written 3.1 years ago by ▴ 50
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda gatk
11 months ago by bestone ▴ 30
6
votes
12
replies
2.0k
views
Help with error in cellranger
Cellranger
updated 11 months ago by 142k • written 12 months ago by ▴ 280
6
votes
7
replies
590
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 3 months ago by 54k • written 3 months ago by • 0
6
votes
1
reply
457
views
16S vs shotgun tools
metagenomics
9 months ago by anasjamshed ▴ 120
6
votes
9
replies
3.0k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 11 months ago by 43k • written 2.3 years ago by ▴ 20
6
votes
5
replies
733
views
Tests for the linear and non-linear relationship between two genes
ode drc correlation regression rnaseq
updated 4 months ago by 82k • written 4 months ago by ▴ 40
6
votes
2
replies
851
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 10 months ago by 43k • written 2.2 years ago by ▴ 180
6
votes
3
replies
569
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler ORA EnrichGo DGE
updated 9 months ago by 4.2k • written 9 months ago by ▴ 100
6
votes
5
replies
502
views
IGV signal visualization, low and high signals
ATAC-seq IGV
updated 11 weeks ago by 100k • written 11 weeks ago by ▴ 30
6
votes
2
replies
734
views
miRNA tool for search targets for genes
mirna targets
updated 10 months ago by 43k • written 2.8 years ago by ★ 1.2k
6
votes
7
replies
1.7k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 12 months ago by 43k • written 6.9 years ago by ▴ 90
6
votes
5
replies
714
views
Log2 transformation is well used, but is there a good paper that can be used as reference ?
TPM log2-transformation r
updated 4 months ago by 87k • written 4 months ago by ▴ 140
6
votes
6
replies
3.2k
views
ChIP-Seq Intensity Analysis
R ChIP-Seq
updated 11 months ago by 43k • written 6.5 years ago by ▴ 20
1,000 results • Page 1 of 20
Recent Votes
Comment: samtools tview symbols
Answer: Server or aws cloud- which one is better for gatk pipeline
Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
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Recent Replies
Comment: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
yeah.. look at that, there is something wrong in your alignment, many reads were mapped in a location but they are all clipped, so somethin…
Comment: Custom Reference panel creation for data imputation from .vcf files by analyst ▴ 50
Hi [Kevin][1]! I have 80 samples of GBS data. I have called variants through GATK pipeline. Now I have to perform imputation. Do I need …
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out? ![enter image description here][…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
Answer: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP …
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message by Max • 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Giulio Genovese ▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list by i.sudbery 19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols by Ruqaiya • 0
What does the star mean then ?
Comment: RNA seq analysis by prifa ▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
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