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9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
6 days ago by vytarasov ▴ 180
1
vote
14
replies
619
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
22 hours ago by hophuquy0944 • 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by • 0 • written 4.8 years ago by ▴ 60
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 12 hours ago by ▴ 170 • written 7.1 years ago by ▴ 240
2
votes
11
replies
660
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
20 hours ago by egascon • 0
0
votes
11
replies
543
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
5 days ago by Tuck898 • 0
0
votes
9
replies
604
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 2 days ago by ★ 2.0k • written 11 days ago by ▴ 140
2
votes
9
replies
698
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 days ago by 161k • written 10 days ago by • 0
0
votes
9
replies
601
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
2 days ago by Arton ▴ 10
4
votes
9
replies
410
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
15 hours ago by Gabriel R. ★ 2.9k
0
votes
9
replies
349
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
1 day ago by njornet ▴ 20
2
votes
8
replies
380
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 5 days ago by 161k • written 5 days ago by ▴ 100
6
votes
7
replies
388
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
5
votes
7
replies
494
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
0
votes
7
replies
442
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 4 days ago by ▴ 20 • written 18 days ago by • 0
0
votes
7
replies
4.2k
views
B allele frequency (BAF)
snp
updated 10 minutes ago by ▴ 10 • written 3.7 years ago by ▴ 90
1
vote
7
replies
390
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
3 days ago by ntsopoul ▴ 60
4
votes
7
replies
422
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
4 days ago by Chen • 0
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by • 0 • written 5.7 years ago by ▴ 20
4
votes
7
replies
446
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 15 hours ago by ▴ 130 • written 2 days ago by ▴ 20
0
votes
6
replies
422
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 4 days ago by 43k • written 7 days ago by • 0
0
votes
6
replies
226
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
6 hours ago by hannes.bongartz • 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 2 days ago by 43k • written 3.9 years ago by • 0
2
votes
6
replies
387
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 5 days ago by • 0
3
votes
6
replies
490
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by ▴ 20 • written 12 days ago by • 0
1
vote
5
replies
261
views
Annotating file using bcftools
annotation plink bcftools
1 day ago by kl ▴ 10
1
vote
5
replies
253
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq deseq2
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
5
replies
283
views
bbmerge (bbmap) ~ error with insert size file output
bbtools bbmerge bbmap
updated 2 days ago by 142k • written 2 days ago by • 0
1
vote
5
replies
216
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos atacseq
updated 2 days ago by 161k • written 2 days ago by ▴ 50
2
votes
5
replies
571
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 5 days ago by ▴ 40 • written 14 days ago by ▴ 30
1
vote
5
replies
276
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 10 hours ago by ★ 2.0k • written 1 day ago by • 0
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
2 days ago by Arton ▴ 10
0
votes
5
replies
334
views
How to convert normalized BigWig file to count matrix?
count-matrix BigWig
5 days ago by feather-W • 0
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 5 days ago by • 0 • written 6.7 years ago by • 0
2
votes
5
replies
494
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 3 days ago by 43k • written 9 days ago by • 0
0
votes
5
replies
319
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by SilhouetteQ • 0
4
votes
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 1 day ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
2
votes
5
replies
269
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 4 days ago by 8.5k • written 4 days ago by • 0
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 6 days ago by • 0 • written 6.5 years ago by ▴ 130
0
votes
4
replies
245
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by 43k • written 2 days ago by • 0
3
votes
4
replies
360
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 1 day ago by 142k • written 1 day ago by 161k
0
votes
4
replies
240
views
Sequencing Depth (Read Depth) Calculations
depth
2 days ago by LucisTheFather • 0
1
vote
4
replies
341
views
Contig assembly task, errors
dna genetics contig assembly
updated 4 days ago by 43k • written 9 days ago by • 0
1
vote
4
replies
237
views
Tool: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes Decimal offtopic Degrees python
updated 1 day ago by 43k • written 2 days ago by ▴ 30
0
votes
4
replies
258
views
Galaxy StringTie error
stringtie galaxy
3 days ago by trkfs • 0
0
votes
4
replies
405
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by beginner123 • 0
2
votes
4
replies
295
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
2 days ago by Esraa • 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 3 days ago by • 0 • written 5.1 years ago by • 0
0
votes
4
replies
307
views
Correlation Analysis
statistics methylation NGS expression
6 days ago by Researcher ▴ 30
184 results • Page 1 of 4
Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
A: Peaks And Nearby Genes
Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
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Recent Replies
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
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