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12,765 results • Page 2 of 256
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10
votes
33
replies
3.9k
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Looking for a tool like fastq screen but for ONT data
gridion nanopore ont minion
updated 10 months ago by 43k • written 5.8 years ago by ★ 1.4k
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 months ago by • 0 • written 6.3 years ago by ▴ 320
147
votes
31
replies
138k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 9 months ago by 43k • written 12.2 years ago by ★ 2.9k
11
votes
31
replies
14k
views
6 follow
How to concatenate multiple fasta file
sequence genome
updated 11 months ago by • 0 • written 5.8 years ago by ▴ 50
105
votes
31
replies
95k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 5 months ago by ▴ 450 • written 12.9 years ago by ★ 5.1k
120
votes
31
replies
200k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 6 months ago by 43k • written 14.1 years ago by 11k
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 6 months ago by 43k • written 14.2 years ago by ★ 1.0k
18
votes
30
replies
10k
views
6 follow
Tool: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina BBMap filterbytile
updated 10 months ago by 43k • written 7.4 years ago by 20k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 6 months ago by 43k • written 14.1 years ago by 18k
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
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 7 weeks ago by 100k • written 8.2 years ago by 43k
16
votes
29
replies
1.8k
views
Gene labels problem in enhanced volcano
R ggplot2 enhancedvolcano
updated 3 months ago by ★ 27k • written 3 months ago by ▴ 120
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 months ago by • 0 • written 8.2 years ago by 20k
20
votes
29
replies
2.5k
views
6 follow
Using bcftools to find unique alt homozygous sites
bcftools
updated 7 months ago by 161k • written 7 months ago by ▴ 70
124
votes
29
replies
7.4k
views
18 follow
What License Do You Use When You Release Code And Data?
software general subjective
updated 6 months ago by 43k • written 14.2 years ago by 7.4k
4
votes
29
replies
11k
views
6 follow
WGCNA soft thresholding problem
WGCNA RNA-Seq soft thresholding data normalization
updated 11 weeks ago by ▴ 10 • written 5.5 years ago by ▴ 40
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 9 weeks ago by ★ 1.2k • written 5.2 years ago by 16k
43
votes
28
replies
5.6k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 6 months ago by 43k • written 14.1 years ago by 11k
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
3 months ago by Jeremy Leipzig 22k
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 14 days ago by • 0 • written 12.8 years ago by ★ 1.7k
3
votes
27
replies
2.6k
views
7 follow
Forum: What server do you use?
HPC AWS
updated 11 months ago by 43k • written 5.8 years ago by ★ 1.9k
197
votes
27
replies
35k
views
20 follow
Forum: Bioinformatics Cartoon
bioinformatics
updated 10 months ago by 43k • written 12.4 years ago by ★ 2.3k
28
votes
27
replies
15k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython python fastq next-gen-sequencing
updated 6 months ago by 43k • written 14.1 years ago by 4.6k
103
votes
27
replies
89k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 12 months ago by • 0 • written 12.0 years ago by ▴ 830
82
votes
27
replies
21k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq atac-seq normalization
updated 6 weeks ago by • 0 • written 4.4 years ago by ▴ 250
73
votes
27
replies
28k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by • 0 • written 10.3 years ago by 100k
26
votes
27
replies
2.2k
views
10 follow
Forum: Determining computer time required
computer hpc time
updated 4 months ago by ★ 6.0k • written 4 months ago by ▴ 40
27
votes
27
replies
10k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp allele biomart dbsnp
updated 6 months ago by 43k • written 14.2 years ago by 54k
77
votes
26
replies
121k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 5 months ago by ★ 2.8k • written 9.1 years ago by ▴ 260
38
votes
26
replies
19k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq ChIP-Seq GO gene ontology
written 8.2 years ago by ▴ 370
21
votes
26
replies
9.8k
views
11 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 9 weeks ago by ▴ 30 • written 4.4 years ago by 8.6k
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 8 months ago by 11k • written 11.3 years ago by ▴ 810
3
votes
26
replies
2.0k
views
6 follow
STAR Genome index Error
STAR
updated 7 months ago by 43k • written 7 months ago by • 0
47
votes
26
replies
4.2k
views
11 follow
Blog: Evolution of Biostars
meta Biostars
updated 8 months ago by ▴ 70 • written 5.2 years ago by 7.1k
24
votes
26
replies
3.7k
views
Tool: ClinCNV: CNV detection from short reads
variant-calling cna cnv
updated 11 months ago by 43k • written 4.6 years ago by ★ 2.9k
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 6 months ago by 43k • written 14.2 years ago by 13k
20
votes
26
replies
3.3k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment fasta image
updated 9 months ago by 21k • written 4.9 years ago by ▴ 210
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 6 months ago by 43k • written 14.1 years ago by 161k
7
votes
25
replies
11k
views
6 follow
Tool: MIGEC: towards error-free profiling of immune repertoires
sequencing-error tcr antibody molecular-barcode
updated 10 months ago by 43k • written 10.0 years ago by 3.5k
69
votes
25
replies
7.1k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 6 months ago by 43k • written 14.2 years ago by ▴ 190
13
votes
25
replies
11k
views
9 follow
Tool: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis sequencing ngs
updated 10 months ago by 43k • written 10.8 years ago by 3.5k
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general subjective
updated 7 months ago by 43k • written 14.3 years ago by 28k
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
18
votes
25
replies
15k
views
13 follow
Easy way to split VCF file by chromosome
sequence TOPMED chromosome Imputation SNP
updated 10 months ago by 161k • written 2.3 years ago by ▴ 30
68
votes
25
replies
16k
views
12 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq SRA
updated 6 months ago by 142k • written 5.2 years ago by ★ 1.4k
51
votes
25
replies
6.9k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service subjective
updated 6 months ago by 43k • written 14.2 years ago by 54k
13
votes
25
replies
4.4k
views
7 follow
VEP output has no gene names
alignment sequencing vep
updated 11 months ago by ★ 2.2k • written 5.8 years ago by ▴ 240
60
votes
25
replies
5.8k
views
8 follow
Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size statistical-power RNA-Seq
updated 11 months ago by 43k • written 3.8 years ago by ▴ 230
38
votes
25
replies
9.2k
views
13 follow
FASTA file of fixed length
sequence fasta
updated 8 months ago by 43k • written 8.1 years ago by ▴ 250
17
votes
25
replies
2.4k
views
Tool: Platform for Bioinformatics Students, Scholars and Scientists
sequence genome
updated 10 months ago by 43k • written 8.2 years ago by ▴ 50
12,765 results • Page 2 of 256
Recent Votes
Answer: Details on salmon index
Comment: zero TPM for many gene including housekeeping when using kallisto
Sequence Alignment from Scratch with BWA
Answer: mitochondrial genome assembly pipeline
Comment: Help! Reconstruction of locus, order contigs
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
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Recent Replies
Comment: Help! Reconstruction of locus, order contigs by GenoMax 142k
Please use `ADD REPLY/ADD COMMENT` when responding to existing content. `SUBMIT ANSWER` is for new answers to the original question.
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…
Comment: Help! Reconstruction of locus, order contigs by BATMAN • 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
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