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13,538 results • Page 4 of 271
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12
votes
22
replies
2.6k
views
Help with error in GATK variant calling
GATK
updated 12 months ago by 43k • written 12 months ago by ▴ 280
27
votes
22
replies
5.7k
views
8 follow
Forum: Recommendations of Linux distros for beginners in bioinformatics
training linux
updated 11 months ago by 43k • written 6.4 years ago by ▴ 810
9
votes
22
replies
9.7k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
10 months ago by vytarasov ▴ 180
28
votes
22
replies
57k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 10 months ago by • 0 • written 11.0 years ago by ▴ 90
138
votes
22
replies
66k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 11 months ago by 87k • written 6.5 years ago by ★ 1.9k
5
votes
22
replies
12k
views
sra toolkit program fastq-dump question.
sratoolkit fastq-dump
updated 10 months ago by 43k • written 9.3 years ago by ▴ 10
24
votes
22
replies
27k
views
11 follow
replace fasta headers with another name in a text file
perl
updated 10 months ago by • 0 • written 9.9 years ago by ▴ 60
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 10 months ago by 43k • written 8.1 years ago by 13k
10
votes
21
replies
3.3k
views
How to interpret heatmap using plotheatmap from deeptools?
ATAC-seq deeptools
9 months ago by Chris ▴ 280
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 5 months ago by • 0 • written 10.0 years ago by ▴ 660
16
votes
21
replies
10.0k
views
7 follow
How to extract bigWig signal for a given bed file?
bigWig
updated 8 months ago by 43k • written 7.6 years ago by ▴ 60
14
votes
21
replies
10k
views
7 follow
HOMER annotatePeaks.pl problem
RNA-Seq ChIP-Seq HOMER
updated 10 months ago by 43k • written 6.6 years ago by ▴ 110
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
4
votes
21
replies
2.7k
views
Limma returned only positive logFC values
edgeR differential-expression deg limma
10 months ago by melissachua90 ▴ 70
15
votes
21
replies
5.6k
views
7 follow
alphafold online availability and use case
alphafold structure prediction
written 2.7 years ago by ▴ 70
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 14 months ago by ▴ 110
43
votes
21
replies
5.5k
views
9 follow
Helping Biostar Grow
biostars
updated 5 months ago by 43k • written 14.1 years ago by 11k
48
votes
21
replies
5.1k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene database
updated 5 months ago by 43k • written 14.1 years ago by 4.9k
23
votes
21
replies
9.0k
views
9 follow
fastest UMAP method
UMAP R
updated 5 months ago by ★ 27k • written 4.5 years ago by ▴ 30
5
votes
21
replies
3.0k
views
How to get my tool on Homebrew ?
homebrew pipeline
updated 10 months ago by 43k • written 4.8 years ago by ▴ 20
12
votes
21
replies
6.7k
views
7 follow
Illumina HumanHT-12 V4.0 expression beadchip
R lumi LIMMA
updated 6 months ago by ★ 7.1k • written 4.1 years ago by ▴ 50
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
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by ▴ 70 • written 9.8 years ago by ▴ 170
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
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 7 months ago by ▴ 210 • written 10.2 years ago by ▴ 750
18
votes
21
replies
4.4k
views
Tool: uQ - small binary FASTQ
Compression FASTQ
updated 10 months ago by 43k • written 7.2 years ago by 13k
13
votes
21
replies
1.8k
views
Practical Haplotype Graph Paths
practical-haplotype-graph PHG
updated 3 months ago by ▴ 200 • written 5 months ago by ▴ 10
22
votes
21
replies
4.8k
views
7 follow
Quick Programming Challenge: Calculate Common And Unique Regions From A List Of Chromosome Segments
programming
updated 5 months ago by 43k • written 14.0 years ago by 18k
60
votes
21
replies
3.8k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome assembly
updated 8 months ago by 54k • written 8 months ago by ▴ 60
0
votes
21
replies
1.1k
views
Expression analysis of LncRNA from RNA-seq data
expression lncrna
12 weeks ago by analyst ▴ 30
12
votes
20
replies
2.5k
views
SEACR and MACS2
MACS2 SEACR
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 10
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 28 days ago by 43k • written 7.6 years ago by ▴ 80
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 26 days ago by ▴ 210 • written 4.3 years ago by ▴ 80
37
votes
20
replies
7.2k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 5 months ago by 43k • written 14.1 years ago by 11k
16
votes
20
replies
14k
views
7 follow
Extracting allele, Genotype from VCF file
vcf
updated 10 months ago by 43k • written 6.0 years ago by ▴ 20
83
votes
20
replies
20k
views
17 follow
How Do Pathway Databases Compare?
pathway database subjective
updated 9 months ago by ▴ 30 • written 13.5 years ago by ▴ 470
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper RNA-seq
6 months ago by langziv ▴ 50
28
votes
20
replies
21k
views
7 follow
how do I run repeat masker
repeatmasker
updated 3 months ago by 11k • written 8.4 years ago by ▴ 80
22
votes
20
replies
4.8k
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 10 months ago by 43k • written 5.5 years ago by ▴ 150
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 28 days ago by 43k • written 6.2 years ago by ▴ 90
1
vote
20
replies
1.6k
views
randomreads.sh only produces reads for chr1 to chr7
randomreads.sh bbmap
updated 9 months ago by 142k • written 10 months ago by ▴ 10
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
29
votes
20
replies
3.7k
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
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
12
votes
20
replies
2.3k
views
Is there a single header file somewhere I can use to read bam?
cpp bam c
updated 11 months ago by 43k • written 5.5 years ago by ▴ 720
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 14.1 years ago by ▴ 70
12
votes
20
replies
1.3k
views
Help with gatk BaseRecalibrator
GATK variant-calling
updated 4 months ago by 43k • written 4 months ago by ▴ 280
0
votes
20
replies
1.6k
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank DNA sequence
4 months ago by Raphaëlle • 0
17
votes
20
replies
1.4k
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
13,538 results • Page 4 of 271
Recent Votes
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: Understanding STAR output (Aligned.out.sam file)
Comment: High Malat-1 expression in single cell data
Comment: removeBatchEffect explained using base R linear models
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Recent Replies
Answer: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases by jared.andrews07 ★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype by GenoMax 142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea() by 1769mkc ★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
Comment: Repeated testing/data mining in RNA Seq by robert.flynn.21 • 0
Thanks! I'll give it a go.
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
Yes, they are very clear about this. The page about the Vignettes says: >"They are not meant as a comprehensive documentation of all the fe…
Comment: Gene density plot by dthorbur ★ 1.9k
This sounds like it would be a simple task in either python or R. Read data in, potentially with a library like `data.table` in `R`, depend…
Answer: HLA-HD tool for genomic imputation by Javier • 0
Hi, I just solved the same error. In my case, it was because I misunderstood the instructions. hlahd.sh -t 4 *-f ~/hlahd.1.7.0/fr…
Comment: Question regarding WGCNA by andres.firrincieli 3.6k
Ok, then. You likely have a scale free topology that look like this: [link][1] In this situation you should pick the power value with an …
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