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1,000 results • Page 5 of 20
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80
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2
replies
54k
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Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 3 months ago by 39k • written 9.9 years ago by 11k
80
votes
15
replies
38k
views
11 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 3.6 years ago by ▴ 20 • written 9.3 years ago by ▴ 750
80
votes
23
replies
4.5k
views
11 follow
Forum: Are we facing a bioinformatician shortage?
salary career
updated 11 weeks ago by 39k • written 8.6 years ago by ★ 3.0k
80
votes
34
replies
4.1k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 4 months ago by 39k • written 8.0 years ago by ▴ 520
80
votes
27
replies
51k
views
23 follow
Renaming Entries In A Fasta File
fasta
updated 7.1 years ago by ▴ 50 • written 10.7 years ago by ▴ 130
80
votes
24
replies
10k
views
18 follow
Which Bioinformatics Journals Do You Follow?
updated 6.7 years ago by 20 • written 13.1 years ago by 27k
80
votes
4
replies
20k
views
Discrimination Between Germline And Somatic Mutations In Tumor Without The Availability Of The Normal Paired Sample
mutation somatic
updated 10.3 years ago by 4.3k • written 10.3 years ago by 4.3k
79
votes
6
replies
42k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam samtools next-gen
updated 14 months ago by 39k • written 11.1 years ago by 4.3k
79
votes
35
replies
8.0k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 1 day ago by • 0 • written 7.5 years ago by ▴ 650
79
votes
22
replies
83k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen sequencing fasta rna r perl
updated 6 months ago by 39k • written 11.6 years ago by ▴ 290
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 21 days ago by 39k • written 9.6 years ago by ★ 7.7k
78
votes
16
replies
43k
views
11 follow
How do you cite a tool that doesn't have a publication?
citation academic style
updated 7.1 years ago by 23k • written 7.2 years ago by ★ 1.1k
78
votes
31
replies
5.8k
views
14 follow
Forum: Do Bad Questions Even Exist?
biostars general education
updated 3 months ago by 39k • written 12.3 years ago by 10k
77
votes
8
replies
12k
views
13 follow
Which program, tool, or strategy do you use to visualize genomic rearrangements?
fusion-genes visualizations rearrangements
updated 8 months ago by 39k • written 7.7 years ago by ★ 1.1k
77
votes
16
replies
32k
views
14 follow
Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier
genbank conversion ncbi taxonomy
updated 6.3 years ago by ★ 1.1k • written 11.8 years ago by ▴ 490
77
votes
20
replies
14k
views
12 follow
Perl Or Python For Comparative Genomics?
bioperl biopython python comparative
updated 5.0 years ago by 5.7k • written 12.7 years ago by ★ 2.0k
77
votes
18
replies
44k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 10 months ago by • 0 • written 13.0 years ago by ★ 1.1k
77
votes
22
replies
21k
views
14 follow
Assessing The Quality Of De Novo Assembled Data
assembly next-gen
updated 8 months ago by 39k • written 11.0 years ago by ★ 2.6k
77
votes
15
replies
9.2k
views
10 follow
Best Bioinformatics Research Images
visualization
updated 11.9 years ago by 7.4k • written 12.0 years ago by 2.3k
77
votes
27
replies
50k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 9 months ago by ▴ 70 • written 9.4 years ago by ▴ 180
77
votes
11
replies
31k
views
9 follow
Star Or Tophat?
rnaseq alignment tophat
updated 2.1 years ago by 39k • written 9.4 years ago by ▴ 970
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 10 weeks ago by 39k • written 5.3 years ago by 85k
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 19 months ago by 39k • written 9.0 years ago by 19k
76
votes
35
replies
26k
views
13 follow
Illumina Instrument Type from fastq?
fastq
updated 27 days ago by ▴ 20 • written 6.9 years ago by 6.5k
76
votes
24
replies
19k
views
18 follow
What Methods Do You Use For Short Read Mapping?
short aligner sequence short
updated 13.2 years ago by ▴ 20 • written 13.2 years ago by ★ 1.0k
76
votes
12
replies
37k
views
8 follow
How Can I Get The Human Chromosome Centromere Position And Chromosome Length In Grch37/Hg19
position ucsc
updated 4.6 years ago by ▴ 100 • written 12.7 years ago by ▴ 260
76
votes
86
replies
26k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression bbmap clumpify pigz storage Tool
updated 5 months ago by 129k • written 6.5 years ago by 18k
75
votes
14
replies
11k
views
10 follow
Tool: karyoploteR: uncircle your genomes
R Tool dataviz karyoploteR NGS
updated 13 months ago by • 0 • written 6.0 years ago by ★ 3.4k
75
votes
22
replies
50k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 9 weeks ago by 39k • written 9.3 years ago by ★ 1.5k
74
votes
24
replies
54k
views
16 follow
How To Sort Bed Format File
bed
updated 7 months ago by 154k • written 10.3 years ago by ▴ 430
74
votes
14
replies
28k
views
12 follow
Forum: Bioinformatics Consulting Thoughts
consulting
updated 11 months ago by 39k • written 13.0 years ago by 4.5k
74
votes
16
replies
4.1k
views
10 follow
Tools & Techniques Bioinformatician Have To Master?
tool subjective
updated 12.2 years ago by ▴ 50 • written 12.2 years ago by ★ 3.3k
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 6 months ago by 39k • written 9.5 years ago by ★ 1.2k
73
votes
25
replies
101k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 11 months ago by 39k • written 8.1 years ago by ▴ 250
73
votes
15
replies
35k
views
8 follow
About Paired-End Sequencing
next-gen sequencing short tool duplicates
updated 12.1 years ago by 4.1k • written 13.1 years ago by 154k
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
73
votes
25
replies
8.4k
views
16 follow
The Five Most Annoying Bioinformatics Problems You Face Every Week?
updated 9.7 years ago by 11k • written 9.7 years ago by ▴ 60
72
votes
14
replies
3.4k
views
12 follow
Forum: Things you wish you knew when entering the bioinformatics field
pitfalls advice forum Forum
updated 2.7 years ago by 7.7k • written 2.7 years ago by ★ 14k
72
votes
18
replies
6.8k
views
17 follow
Forum: What Is One Book Every Bioinformatician Should Read?
books
updated 3 months ago by 39k • written 9.9 years ago by 7.7k
72
votes
20
replies
24k
views
11 follow
Parsing Ncbi Taxonomic Tree?
ncbi taxonomy python tree
updated 5 months ago by 39k • written 11.6 years ago by ▴ 350
72
votes
28
replies
5.4k
views
10 follow
Forum: Bioinformatics commercial services as a risk factor for scientific misconduct
commercial-services ethics misconduct
updated 11 months ago by 39k • written 8.4 years ago by ▴ 90
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 3 months ago by 39k • written 10.3 years ago by 33k
72
votes
48
replies
7.1k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 3 months ago by 39k • written 12.1 years ago by 13k
72
votes
18
replies
54k
views
13 follow
Extracting Multiple Fasta Sequences At A Time From A File Containing Many Sequences
fasta sequence parsing perl
updated 12.6 years ago by 6.0k • written 12.6 years ago by ▴ 110
72
votes
12
replies
3.8k
views
7 follow
Does Pre-Publishing Open Source Algorithms Hurt Chances Of Getting Published?
publication algorithm
updated 10 months ago by 39k • written 11.7 years ago by ▴ 570
71
votes
7
replies
12k
views
6 follow
What Should I Use Blat For?
alignment
updated 10.5 years ago by 11k • written 10.5 years ago by ★ 4.1k
71
votes
15
replies
19k
views
12 follow
Counting N'S Within Fasta
fasta counts perl
updated 5.0 years ago by 20 • written 11.2 years ago by 5.1k
71
votes
17
replies
32k
views
14 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 4 months ago by ★ 2.9k • written 9.1 years ago by ▴ 600
71
votes
71
replies
25k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano plot ggplot2 ggrepel bioconductor Tool
updated 7 months ago by ▴ 40 • written 4.7 years ago by 85k
1,000 results • Page 5 of 20
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Comment: featureCounts: ERROR: failed to find the gene identifier attribute
Answer: bedtools intersect zero output
Answer: What is the best way to clean bulk RNA-seq data?
What does <*> mean in a vcf file?
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Comment: featureCounts: ERROR: failed to find the gene identifier attribute by v.berriosfarias ▴ 90
yes I provided the column names just for showing it was a gtf file. Thanks for the recommendation of the SAF file. It worked!
Answer: What is the best way to clean bulk RNA-seq data? by ATpoint 72k
For the sake of simplicity and because it well stood the test of time I always use use `edgeR::filterByExpr()` which has reasonable default…
Comment: Is there anyway to cancel CPM normalization? by JACKY ▴ 80
hmm I'm not sure what you mean, but this is my code: GetGeneLength <- function(counts = counts){ ensembl = useEnsembl(bio…
Answer: how to intersect multiple bed files and get results in uncollapsed genomic inter by Alex Reynolds 35k
Generally, you could use `bedops --chop` with some piping and process substitutions with `bedmap` to get count/ID/score data: bedops -…
Comment: IGV grey vs white lines by Mohd • 0
Hi, Thanks alot, This was really helpful and worked, however, I am looking for references where I can find how the minimap assign the MAPQ …
Comment: Single cell chemistry by swbarnes2 13k
You could still trick cellranger into processing them. Use umi tools to determine what the cell barcodes really are, (and see if they make…
Comment: Single cell chemistry by swbarnes2 13k
Well, A is a real letter. I don't know off the top of my head how cellranger deals with N's. But if the cell barcodes didn't match the v2 …
Comment: Single cell chemistry by David • 0
That's the question, I think these data are not a useful entry for cellranger. Do you know if there is any other compatible software for th…
Comment: Single cell chemistry by David • 0
I tried to add an "N" to the end of every read in R1 and cellranger did not found any barcode, results but no cells, I did it again adding …
Answer: ABySS genome assembler by shelkmike ▴ 920
You can use Kmergenie (http://kmergenie.bx.psu.edu/). It is a special tool for finding the optimal k-mer length.
Comment: Retrieving allele-specific information for a variant using VEP annotation by Ram 39k
It is pretty trivial to do the COSMIC annotation without tools such as VEP - download their coding and non-coding VCFs, normalize (decompos…
Answer: Perl. How to extract CDS and gene sequence in a specified interval from GenBank by Fungi-Beware! • 0
Figured I need to attach an expected OUTPUT result. Should look something like this: ---------- ``` LOCUS 19 58617616 bp DNA HTG 23-NOV-2…
Comment: Upstream pseudogene causing MAPQ 0 and exclusion during variant calling by Joel Wallenius ▴ 120
Yes, well... surely it's better with some FPs and TPs than nothing at all, eh. Is there another way to do this? Hmm...
Comment: Demultiplexing bam file by hasani.iut6 ▴ 60
No. All of the Ids are "13.02.1402_POOL2". Do you think my bam file is not correct?
Comment: Demultiplexing bam file by hasani.iut6 ▴ 60
Yes, you're right, I know the bam file consists of multiple samples (It should be between 30 to 40 samples) and the size of the bam file is…
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