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12,702 results • Page 4 of 255
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38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 11 months ago by 43k • written 8.1 years ago by 13k
10
votes
21
replies
3.4k
views
How to interpret heatmap using plotheatmap from deeptools?
ATAC-seq deeptools
9 months ago by Chris ▴ 280
5
votes
21
replies
3.0k
views
How to get my tool on Homebrew ?
homebrew pipeline
updated 11 months ago by 43k • written 4.9 years ago by ▴ 20
39
votes
21
replies
14k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 11 months ago by 43k • written 5.6 years ago by 8.6k
80
votes
21
replies
37k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 6 months ago by • 0 • written 10.1 years ago by ▴ 660
4
votes
21
replies
2.3k
views
6 follow
how to automate this process
python plantCARE
updated 10 months ago by 43k • written 7.3 years ago by ▴ 680
16
votes
21
replies
10k
views
7 follow
How to extract bigWig signal for a given bed file?
bigWig
updated 9 months ago by 43k • written 7.6 years ago by ▴ 60
43
votes
21
replies
5.5k
views
9 follow
Helping Biostar Grow
biostars
updated 6 months ago by 43k • written 14.1 years ago by 11k
24
votes
21
replies
7.6k
views
9 follow
News: Misunderstood parameter of NCBI BLAST
blast alignment
updated 11 months ago by 43k • written 5.6 years ago by ★ 3.4k
12
votes
21
replies
6.7k
views
7 follow
Illumina HumanHT-12 V4.0 expression beadchip
R lumi LIMMA
updated 6 months ago by ★ 7.2k • written 4.1 years ago by ▴ 50
15
votes
21
replies
5.6k
views
7 follow
alphafold online availability and use case
alphafold structure prediction
written 2.8 years ago by ▴ 70
4
votes
21
replies
2.7k
views
Limma returned only positive logFC values
edgeR differential-expression deg limma
10 months ago by melissachua90 ▴ 70
22
votes
21
replies
4.9k
views
7 follow
Quick Programming Challenge: Calculate Common And Unique Regions From A List Of Chromosome Segments
programming
updated 6 months ago by 43k • written 14.1 years ago by 18k
13
votes
21
replies
3.1k
views
6 follow
Aberrant splicing in bulk RNAseq
aberrant-splicing transcript isoform exon
updated 11 months ago by • 0 • written 15 months ago by ▴ 130
18
votes
21
replies
4.5k
views
Tool: uQ - small binary FASTQ
Compression FASTQ
updated 10 months ago by 43k • written 7.2 years ago by 13k
15
votes
21
replies
1.1k
views
Expression analysis of LncRNA from RNA-seq data
expression lncrna
3 months ago by analyst ▴ 50
81
votes
21
replies
43k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 8 months ago by ▴ 210 • written 10.3 years ago by ▴ 750
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 10 months ago by 43k • written 12.1 years ago by ★ 1.5k
14
votes
21
replies
10k
views
7 follow
HOMER annotatePeaks.pl problem
RNA-Seq ChIP-Seq HOMER
updated 11 months ago by 43k • written 6.6 years ago by ▴ 110
16
votes
20
replies
14k
views
7 follow
Extracting allele, Genotype from VCF file
vcf
updated 10 months ago by 43k • written 6.1 years ago by ▴ 20
21
votes
20
replies
9.6k
views
11 follow
Laptops for bioinformatics
hardware Laptops
updated 10 months ago by 4.2k • written 18 months ago by ▴ 40
18
votes
20
replies
4.5k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 5 weeks ago by 43k • written 7.6 years ago by ▴ 80
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 5 weeks ago by 43k • written 6.3 years ago by ▴ 90
83
votes
20
replies
20k
views
17 follow
How Do Pathway Databases Compare?
pathway database subjective
updated 10 months ago by ▴ 30 • written 13.5 years ago by ▴ 470
1
vote
20
replies
1.6k
views
randomreads.sh only produces reads for chr1 to chr7
randomreads.sh bbmap
updated 10 months ago by 142k • written 10 months ago by ▴ 10
29
votes
20
replies
3.8k
views
Tool: FastQt : a clone of FastQC in C++/Qt
fastqc Cpp fastq Qt
updated 10 months ago by 43k • written 7.4 years ago by ★ 2.4k
28
votes
20
replies
21k
views
7 follow
how do I run repeat masker
repeatmasker
updated 4 months ago by 11k • written 8.4 years ago by ▴ 80
49
votes
20
replies
2.1k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 4 months ago by ★ 2.6k • written 4 months ago by ★ 27k
0
votes
20
replies
1.7k
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank DNA sequence
4 months ago by Raphaëlle • 0
14
votes
20
replies
6.7k
views
7 follow
Tool Recommendations For Human Genome Assembly
assembly human-genome
updated 11 months ago by 43k • written 11.2 years ago by ▴ 800
12
votes
20
replies
1.3k
views
Help with gatk BaseRecalibrator
GATK variant-calling
updated 5 months ago by 43k • written 5 months ago by ▴ 280
12
votes
20
replies
2.3k
views
Is there a single header file somewhere I can use to read bam?
cpp bam c
updated 12 months ago by 43k • written 5.6 years ago by ▴ 720
17
votes
20
replies
1.5k
views
What is the best way to compute genetic distances between FASTQ files?
genetic-distance fastq
updated 6 months ago by 142k • written 6 months ago by ▴ 10
37
votes
20
replies
7.3k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 6 months ago by 43k • written 14.1 years ago by 11k
22
votes
20
replies
4.9k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam bqsr
updated 11 months ago by 43k • written 5.6 years ago by ▴ 150
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 5 weeks ago by ▴ 210 • written 4.3 years ago by ▴ 80
18
votes
20
replies
4.2k
views
9 follow
Is There Any Useful Information To Be Gathered Analyzing The Genomes Of Different Populations Of Cicadas?
project education
updated 6 months ago by 43k • written 14.2 years ago by ▴ 70
2
votes
20
replies
2.4k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
8 months ago by Maxine ▴ 40
7
votes
20
replies
2.1k
views
Forum: NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR RNA-Seq TopHat
updated 12 months ago by 43k • written 3.3 years ago by ▴ 10
15
votes
20
replies
1.8k
views
Bbtools callvariant multisample mode, + base recalibration
Bbtools
5 months ago by Axzd ▴ 70
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper RNA-seq
7 months ago by langziv ▴ 50
12
votes
20
replies
2.6k
views
SEACR and MACS2
MACS2 SEACR
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 10
25
votes
19
replies
8.2k
views
10 follow
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork R pathway-enrichment
updated 11 months ago by 43k • written 6.2 years ago by ★ 1.3k
15
votes
19
replies
8.8k
views
6 follow
Tool: Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf database genome variation
updated 10 months ago by 43k • written 11.1 years ago by 12k
75
votes
19
replies
3.5k
views
11 follow
Blog: A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 10 weeks ago by 4.2k • written 8 months ago by ▴ 30
3
votes
19
replies
1.6k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS error panels sequencing
updated 10 months ago by 10k • written 10 months ago by ▴ 20
12
votes
19
replies
5.8k
views
how to identify CDR region in antibody sequence
CDR antibody
updated 11 weeks ago by • 0 • written 23 months ago by ▴ 50
93
votes
19
replies
60k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 11 months ago by 43k • written 13.7 years ago by ★ 2.6k
66
votes
19
replies
51k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 11 months ago by 43k • written 11.3 years ago by ★ 3.6k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 10 months ago by 43k • written 11.0 years ago by ▴ 250
12,702 results • Page 4 of 255
Recent Votes
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
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
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Popular Question to finswimmer 16k
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Recent Replies
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: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
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.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
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