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1,000 results • Page 4 of 20
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4
votes
3
replies
407
views
Single cell analysis of Cancer
cancer single-cell RNA-seq
updated 3 months ago by 142k • written 3 months ago by ▴ 20
4
votes
2
replies
675
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 7 months ago by ★ 1.5k • written 7 months ago by ▴ 100
4
votes
6
replies
1.9k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 10 months ago by 142k • written 10 months ago by • 0
4
votes
3
replies
338
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 3 months ago by ★ 1.8k • written 3 months ago by ▴ 10
4
votes
11
replies
1.9k
views
PCA WITH PLINK
PLINK
updated 9 months ago by 88k • written 9 months ago by • 0
4
votes
6
replies
875
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 6 weeks ago by 43k • written 5 months ago by ▴ 30
4
votes
3
replies
724
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 9 months ago by 11k • written 9 months ago by ▴ 10
4
votes
7
replies
1.1k
views
Statistical test to compare data across timepoints
Statistics
updated 7 months ago by 4.6k • written 7 months ago by ▴ 20
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV WGS
updated 10 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
6
replies
2.5k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 11 months ago by • 0 • written 21 months ago by ▴ 20
4
votes
6
replies
2.7k
views
Convert Nanopore Fast5 files to Fasta format
fast5 fasta Nanopore
11 months ago by Sowmya Pulapet ▴ 70
4
votes
5
replies
1.2k
views
tranfering sam file easy and fast way
SAM RNA-seq hisat2
updated 8 months ago by 43k • written 2.4 years ago by • 0
4
votes
5
replies
1.1k
views
VEP run with --af_gnomadg refuses to provide allele frequencies for extremely rare variants
vep gnomad
updated 9 months ago by ▴ 60 • written 9 months ago by 22k
4
votes
6
replies
962
views
Open-Source software. Good or bad for the market?
genomic-analysis software
updated 12 months ago by 43k • written 6.2 years ago by • 0
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 50
4
votes
14
replies
1.2k
views
remove white space in fastq file
fastq
updated 4 months ago by 142k • written 4 months ago by • 0
4
votes
8
replies
627
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
4
votes
9
replies
2.7k
views
Blast+ remote database names
blast remote databases Blastplus
updated 10 months ago by 142k • written 2.4 years ago by • 0
4
votes
6
replies
662
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
5 months ago by Tihana ▴ 10
4
votes
5
replies
408
views
Filter out miRNA from ncRNA dataset
bowtie bowtie2 miRNA filtering ncRNA
updated 12 weeks ago by 82k • written 12 weeks ago by ▴ 10
4
votes
7
replies
632
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 4 weeks ago by 43k • written 4 weeks ago by ▴ 20
3
votes
8
replies
938
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 142k • written 10 months ago by • 0
3
votes
14
replies
1.2k
views
How to extract specific region from multiple bam files and merge the outputs into single bam?
bam rna-seq
updated 6 months ago by 142k • written 6 months ago by ▴ 770
3
votes
2
replies
321
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 5 weeks ago by 43k • written 10 weeks ago by ▴ 20
3
votes
4
replies
311
views
Truncated metadata file report from ENA Portal API
ena python
5 days ago by Giulia • 0
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap wgcna
updated 7 months ago by 43k • written 2.6 years ago by ▴ 40
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
3
votes
4
replies
681
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 270
3
votes
3
replies
259
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 1 day ago by 43k • written 15 days ago by • 0
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career bio
updated 12 months ago by 43k • written 6.2 years ago by ▴ 20
3
votes
5
replies
944
views
Ensembl site unresponsive in clusterProfiler analyses
parallell clusterProfiler R
updated 8 months ago by ▴ 510 • written 8 months ago by • 0
3
votes
5
replies
800
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run DiffBind ChIP-seq
updated 5 months ago by ★ 2.0k • written 5 months ago by ▴ 10
3
votes
6
replies
1.1k
views
Very different QUAL scores on VCFs of same sample using different methods
deepvariant clara-parabricks haplotypecaller vcf
10 months ago by Victor ▴ 10
3
votes
2
replies
180
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 2 days ago by 82k • written 2 days ago by • 0
3
votes
3
replies
516
views
Need Control Gene Count Files
R RNA-Seq TCGA
updated 6 months ago by ▴ 20 • written 6 months ago by ▴ 30
3
votes
6
replies
2.1k
views
Biopython TimeExceptionError how to handle?
biopython entrez
updated 12 months ago by 43k • written 6.5 years ago by ▴ 80
3
votes
6
replies
773
views
No genes mapped in clusterprofiler gseGO
R clusterProfiler gseGO GSEA
4 months ago by jon50250 • 0
3
votes
3
replies
550
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 25 days ago by 14k • written 26 days ago by ▴ 580
3
votes
2
replies
341
views
Illumina reads to be processed and prepared for reference genome alignment
genome alignment trimming next-gen Illumina
updated 3 months ago by ★ 1.2k • written 3 months ago by • 0
3
votes
7
replies
3.3k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter vcftools sequencing
updated 10 months ago by 43k • written 4.2 years ago by ▴ 10
3
votes
9
replies
701
views
STARsolo seg fault without readMapNumber flag
STAR RNA-seq STARsolo Velocyto
updated 6 months ago by 43k • written 6 months ago by ▴ 420
3
votes
1
reply
572
views
automatic clustering annotation using python
automatic-clustering single-cell
updated 10 months ago by ★ 1.6k • written 10 months ago by ▴ 10
3
votes
3
replies
820
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 9 months ago by 3.6k • written 9 months ago by ▴ 720
3
votes
6
replies
3.1k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk variant calling sureselect
updated 9 months ago by • 0 • written 4.2 years ago by ▴ 750
3
votes
6
replies
3.3k
views
samtools sort not working when using multiple threads
samtools bam
updated 11 months ago by 43k • written 2.3 years ago by ▴ 10
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 7 days ago by • 0 • written 5.5 years ago by 8.5k
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 28 days ago by 43k • written 4.5 years ago by ▴ 10
3
votes
1
reply
402
views
FastQC duplicates questions
FastQC RNA-seq
8 months ago by Beth ▴ 10
3
votes
5
replies
693
views
ATAC-Seq and featureCounts
ATAC-Seq featureCounts
updated 4 months ago by 82k • written 4 months ago by ▴ 10
3
votes
5
replies
1.4k
views
AlphaMissense Plugin VEP
Plugin VEP Alphamissense
updated 7 months ago by 43k • written 7 months ago by ▴ 10
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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