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12,645 results • Page 4 of 253
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38
votes
8
replies
1.7k
views
6 follow
News: What happens when a bioinformatician has his own genome sequenced for $300?
DNAseq DNA WGS
updated 11 months ago by 35k • written 11 months ago by 11k
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 21 hours ago by ▴ 170 • written 7.1 years ago by ▴ 240
38
votes
11
replies
4.1k
views
7 follow
Python Documentation Tools
python
updated 11 months ago by 43k • written 14.0 years ago by ★ 3.3k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 18 days ago by 19k • written 20 days ago by ▴ 580
38
votes
17
replies
3.3k
views
7 follow
Forum: Why does bioinformatics use a special format like a BAM file instead of a database like SQLite?
sam bam samtools
updated 11 months ago by 43k • written 3.7 years ago by ▴ 250
38
votes
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed ensembl bedops gtf
updated 11 weeks ago by 35k • written 7.8 years ago by ▴ 260
38
votes
14
replies
9.1k
views
8 follow
Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
ensembl python biopython genome
updated 6 months ago by 43k • written 14.1 years ago by ▴ 270
37
votes
9
replies
4.5k
views
8 follow
What are the advantages of using the T2T as a reference vs GRCh38 today?
reference GRCh38 t2t calling variant
updated 11 months ago by 4.2k • written 13 months ago by ▴ 170
37
votes
5
replies
14k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 5 weeks ago by ▴ 60 • written 2.9 years ago by ★ 1.0k
37
votes
11
replies
33k
views
6 follow
Sjdboverhang Option In Star
updated 10 months ago by ▴ 90 • written 10.2 years ago by ★ 3.1k
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 8 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
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
36
votes
34
replies
2.9k
views
9 follow
Forum: New to bioinformatics.....
gene
updated 12 months ago by 43k • written 6.1 years ago by • 0
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen RNA-Seq
updated 4 months ago by ▴ 60 • written 9.7 years ago by ▴ 90
36
votes
16
replies
14k
views
8 follow
How to identify 16s sequences from binning data(contigs)?
genome Assembly sequence blast
updated 10 months ago by ▴ 90 • written 8.6 years ago by ▴ 110
36
votes
17
replies
3.7k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 6 months ago by 43k • written 14.2 years ago by 28k
36
votes
13
replies
7.3k
views
8 follow
How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
data galaxy
written 13.0 years ago by ▴ 520
35
votes
11
replies
45k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 4 months ago by 43k • written 12.0 years ago by ▴ 160
35
votes
14
replies
44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 7 months ago by ▴ 130 • written 7.9 years ago by ★ 5.3k
35
votes
10
replies
16k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq peak-calling
updated 6 months ago by 43k • written 14.1 years ago by ★ 1.4k
35
votes
15
replies
12k
views
10 follow
How to select an aligner?
RNA-Seq next-gen alignment
updated 4 months ago by • 0 • written 6.0 years ago by ▴ 710
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
34
votes
23
replies
22k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq genome
updated 8 months ago by ▴ 120 • written 6.1 years ago by ▴ 680
34
votes
8
replies
2.7k
views
9 follow
Forum: Bioinformatician, a jack of all trades, but in the eye of the CV-beholder a master of none? How can your CV reflect the diverse skills that you have …
cv industry career
updated 11 months ago by 43k • written 4.6 years ago by ▴ 300
34
votes
16
replies
20k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 weeks ago by ▴ 30 • written 7.6 years ago by ▴ 310
34
votes
22
replies
3.0k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
Bioinformatician COVID-19
updated 11 months ago by 43k • written 4.0 years ago by ▴ 10
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 29 days ago by ▴ 10 • written 10.3 years ago by ▴ 180
34
votes
9
replies
11k
views
7 follow
Tool: Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 10 months ago by 43k • written 10.2 years ago by 24k
33
votes
10
replies
36k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq ensembl
updated 10 months ago by 43k • written 9.8 years ago by ▴ 540
33
votes
9
replies
10k
views
10 follow
Which C++ Libraries Are Best For Dealing With Fastq Files?
next-gen-sequencing fastq c
updated 6 months ago by 43k • written 14.2 years ago by 22k
33
votes
3
replies
15k
views
Tool: Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
bwa ngs
updated 10 months ago by 43k • written 11.2 years ago by 33k
33
votes
12
replies
1.1k
views
7 follow
Forum: Nextflow and self-made pipelines opinion
nextflow pipeline data-analysis
11 weeks ago by karlaarz ▴ 110
33
votes
23
replies
4.3k
views
8 follow
Forum: Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF file-format genomics
updated 11 months ago by 22k • written 11 months ago by 4.2k
32
votes
4
replies
9.4k
views
Fastq Qualities For Solexa/Illumina
sequencing-quality next-gen-sequencing fastq
updated 6 months ago by 43k • written 14.1 years ago by 161k
32
votes
13
replies
10.0k
views
11 follow
Any Recommendations For Statistical Genetics Texts?
genetics statistics gwas
updated 4 months ago by • 0 • written 13.8 years ago by ▴ 180
31
votes
14
replies
24k
views
7 follow
Difference between tSNE and PCA analysis
next-gen rna-seq
updated 12 weeks ago by 22k • written 6.3 years ago by ▴ 160
31
votes
22
replies
13k
views
6 follow
Tool: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ SeqKit FASTA
updated 11 months ago by 43k • written 7.6 years ago by 8.5k
31
votes
41
replies
2.8k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 11 months ago by 43k • written 4.2 years ago by ▴ 40
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp amino-acids
updated 4 months ago by ▴ 80 • written 12.4 years ago by ▴ 110
31
votes
11
replies
5.7k
views
6 follow
Assessing Cluster Reliability/Stability In Microarray Experiments
clustering microarray gene
updated 6 months ago by 43k • written 14.1 years ago by ★ 2.2k
31
votes
30
replies
15k
views
6 follow
Tool: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene RNA-Seq Venn-diagram PCA
updated 10 months ago by 43k • written 6.0 years ago by ▴ 450
31
votes
11
replies
6.7k
views
8 follow
Basics Of Systems Biology...
network
updated 10 months ago by • 0 • written 13.8 years ago by ★ 1.5k
31
votes
16
replies
2.2k
views
8 follow
Forum: What is in your opinion the current state-of-the-art sequencing platform for genomic assembly (Nov 2019)
next-gen-sequencing assembly genome
updated 11 months ago by 43k • written 4.6 years ago by ★ 5.1k
31
votes
8
replies
13k
views
Experiences With Clc Genomics Workbench (Or Other Commercial Tools) For Next-Gen Sequencing
next-gen-sequencing
updated 6 months ago by 43k • written 14.1 years ago by 100k
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna rRNA metagenomics
updated 7 weeks ago by 43k • written 13.6 years ago by ▴ 650
31
votes
8
replies
8.3k
views
9 follow
Notepad and word will not read Fastq or FASTA files
software-error fastq
written 9.2 years ago by • 0
30
votes
13
replies
3.7k
views
11 follow
Forum: what is your daily must see bioinformatics web site?
learn technology
updated 11 months ago by 43k • written 9.7 years ago by 9.7k
30
votes
15
replies
10k
views
7 follow
Tool: Snakemake--Python-Based Workflow Management
workflow snakemake python
updated 10 months ago by 43k • written 10.5 years ago by 26k
30
votes
6
replies
13k
views
What Are Some Good Free Bioinformatics And Computational Biology Books?
books online
updated 6 months ago by 43k • written 14.1 years ago by ★ 1.0k
30
votes
18
replies
16k
views
8 follow
Is It Possible For Two Different Affymetrix Probe Set Id To Have Common Annotations To Same Gene ?
microarray annotation affymetrix probeset
updated 6 months ago by 43k • written 14.2 years ago by 18k
12,645 results • Page 4 of 253
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
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…
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