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1,000 results • Page 4 of 20
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40
votes
6
replies
15k
views
7 follow
Mapping Ensembl Gene IDs with dot suffix
ensembl gene biomart bioconductor R
updated 9 months ago by 11k • written 6.1 years ago by ▴ 290
40
votes
19
replies
9.6k
views
12 follow
Is There A Site Where Call For Papers And Conferences Are Listed In One Place?
papers conference
updated 5 months ago by 43k • written 14.1 years ago by ▴ 270
39
votes
6
replies
19k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 11 months ago by 43k • written 6.6 years ago by ★ 3.5k
39
votes
15
replies
23k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene r
updated 5 months ago by 43k • written 14.1 years ago by ▴ 790
39
votes
21
replies
13k
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 5.5 years ago by 8.5k
39
votes
18
replies
6.0k
views
10 follow
Any Open Notebook Science In Bioinformatics?
open-notebook
updated 5 months ago by 43k • written 14.0 years ago by ▴ 380
39
votes
11
replies
9.1k
views
11 follow
Where Can I Get The Secondary Structure Of A Protein?
protein structure sequence
updated 6 months ago by 43k • written 14.2 years ago by 28k
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
11 weeks ago by Jeremy Leipzig 22k
39
votes
23
replies
34k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 7 months ago by ▴ 40 • written 2.8 years ago by ▴ 130
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 2 days ago by 43k • written 6.7 years ago by ★ 1.3k
39
votes
16
replies
36k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 3 months ago by 141k • written 3.7 years ago by ▴ 160
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 8.0 years ago by 13k
38
votes
11
replies
4.1k
views
7 follow
Python Documentation Tools
python
updated 10 months ago by 43k • written 13.9 years ago by ★ 3.3k
38
votes
25
replies
9.1k
views
13 follow
FASTA file of fixed length
sequence fasta
updated 7 months ago by 43k • written 8.0 years ago by ▴ 250
38
votes
14
replies
9.0k
views
8 follow
Is There A Non-Perl Alternative To Accessing Ensembl'S Api?
ensembl python biopython genome
updated 5 months ago by 43k • written 14.1 years ago by ▴ 270
38
votes
26
replies
18k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq ChIP-Seq GO gene ontology
written 8.2 years ago by ▴ 370
38
votes
17
replies
3.2k
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 10 months ago by 43k • written 3.7 years ago by ▴ 250
38
votes
19
replies
11k
views
Tool: Excel add-in for DNA/RNA string manipulations
sequence DNA RNA Excel
updated 10 months ago by 43k • written 8.1 years ago by ▴ 140
38
votes
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed ensembl bedops gtf
updated 7 weeks ago by 35k • written 7.7 years ago by ▴ 260
38
votes
7
replies
2.2k
views
News: 2 last seats available - 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Transcriptomics DNA-Seq Variant-Calling RNA-Seq
8 months ago by David Langenberger 11k
38
votes
8
replies
1.6k
views
6 follow
News: What happens when a bioinformatician has his own genome sequenced for $300?
DNAseq DNA WGS
updated 10 months ago by 35k • written 10 months ago by 11k
37
votes
16
replies
4.0k
views
9 follow
Forum: Sanger sequencing is no longer the gold standard?
Sanger NGS
updated 11 months ago by 43k • written 6.5 years ago by ▴ 220
37
votes
20
replies
7.2k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 5 months ago by 43k • written 14.0 years ago by 11k
37
votes
9
replies
4.4k
views
8 follow
What are the advantages of using the T2T as a reference vs GRCh38 today?
reference GRCh38 t2t calling variant
updated 10 months ago by 4.2k • written 12 months ago by ▴ 170
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 9 days ago by ▴ 60 • written 2.9 years ago by ★ 1.0k
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 7 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
36
votes
34
replies
2.8k
views
9 follow
Forum: New to bioinformatics.....
gene
updated 11 months ago by 43k • written 6.1 years ago by • 0
36
votes
39
replies
4.1k
views
11 follow
Forum: Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast RNA-Seq alignment next-gen-sequencing
updated 11 months ago by 43k • written 6.4 years ago by ▴ 130
36
votes
17
replies
3.6k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 5 months ago by 43k • written 14.1 years ago by 28k
36
votes
13
replies
7.2k
views
8 follow
How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
data galaxy
written 12.9 years ago by ▴ 520
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
11
replies
32k
views
6 follow
Sjdboverhang Option In Star
updated 9 months ago by ▴ 90 • written 10.2 years ago by ★ 3.1k
36
votes
16
replies
14k
views
8 follow
How to identify 16s sequences from binning data(contigs)?
genome Assembly sequence blast
updated 9 months ago by ▴ 90 • written 8.6 years ago by ▴ 110
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 11 months ago by 141k • written 10.4 years ago by 20k
35
votes
10
replies
16k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq peak-calling
updated 5 months ago by 43k • written 14.0 years ago by ★ 1.4k
35
votes
15
replies
12k
views
10 follow
How to select an aligner?
RNA-Seq next-gen alignment
updated 3 months ago by • 0 • written 5.9 years ago by ▴ 710
35
votes
14
replies
43k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 6 months ago by ▴ 130 • written 7.8 years ago by ★ 5.3k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 9 months ago by 43k • written 10.9 years ago by ▴ 250
34
votes
22
replies
2.9k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
Bioinformatician COVID-19
updated 10 months ago by 43k • written 3.9 years ago by ▴ 10
34
votes
16
replies
20k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 4 weeks ago by ▴ 30 • written 7.5 years ago by ▴ 310
34
votes
5
replies
2.3k
views
Forum: what we should reply when we are asked do you have any question?
career interview
updated 11 months ago by 43k • written 6.9 years ago by ★ 4.3k
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 10 months ago by 43k • written 4.5 years ago by ▴ 300
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 9 hours ago by ▴ 10 • written 10.2 years ago by ▴ 180
34
votes
9
replies
11k
views
7 follow
Tool: Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 9 months ago by 43k • written 10.2 years ago by 24k
34
votes
11
replies
44k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 3 months ago by 43k • written 11.9 years ago by ▴ 160
33
votes
3
replies
14k
views
Tool: Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
bwa ngs
updated 9 months ago by 43k • written 11.1 years ago by 33k
33
votes
23
replies
21k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq genome
updated 7 months ago by ▴ 120 • written 6.1 years ago by ▴ 670
33
votes
9
replies
10k
views
10 follow
Which C++ Libraries Are Best For Dealing With Fastq Files?
next-gen-sequencing fastq c
updated 5 months ago by 43k • written 14.1 years ago by 22k
33
votes
10
replies
35k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq ensembl
updated 9 months ago by 43k • written 9.8 years ago by ▴ 540
33
votes
23
replies
4.1k
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 10 months ago by 22k • written 10 months ago by 4.2k
1,000 results • Page 4 of 20
Recent Votes
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Done. Thank you.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by GenoMax 141k
Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by BioinfGuru ★ 1.7k
Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
Comment: Downloading the raw microarray data from GEO by GenoMax 141k
No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
Comment: Cellranger count error: Input FASTQ file ended prematurely by GenoMax 141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely by bp22 ▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by Ram 43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately? by Ram 43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by _quantum_girl_ ▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis by BioinfGuru ★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis by Mohamed Abderrahmane ▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
Comment: Illumina reads preprocessing best practice for snp calling applications by Enrique • 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster? by ATpoint 81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis by joe ▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort by ATpoint 81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
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