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148
votes
35
replies
59k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 1.6k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
145
votes
34
replies
52k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 3 months ago by 39k • written 10.1 years ago by 5.9k
145
votes
56
replies
7.5k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 3 months ago by 39k • written 10.2 years ago by 98k
144
votes
62
replies
9.6k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 3 months ago by 39k • written 12.3 years ago by ★ 2.9k
143
votes
14
replies
20k
views
15 follow
What Are The Classic Papers In Bioinformatics?
literature papers history
updated 2.2 years ago by 21k • written 12.6 years ago by 18k
143
votes
30
replies
128k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line command-line fasta list bash
updated 8 months ago by 39k • written 11.3 years ago by ★ 2.9k
143
votes
33
replies
28k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 4.2 years ago by ▴ 50 • written 13.0 years ago by 13k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 13 months ago by 39k • written 8.5 years ago by ★ 1.6k
142
votes
14
replies
165k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 3.5 years ago by ★ 2.1k • written 13.2 years ago by 154k
139
votes
13
replies
21k
views
Alignment and mapping
alignment next-gen mapping
updated 7.2 years ago by 8.3k • written 7.2 years ago by ▴ 720
138
votes
42
replies
20k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 10 weeks ago by ★ 2.9k • written 10.0 years ago by ★ 1.6k
138
votes
21
replies
68k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
2.7 years ago by Malachi Griffith 19k
136
votes
25
replies
77k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 14 months ago by 39k • written 11.1 years ago by ★ 4.2k
136
votes
29
replies
6.6k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 13 months ago by 39k • written 12.4 years ago by 21k
136
votes
26
replies
23k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix perl genomics
updated 3 months ago by 39k • written 11.4 years ago by ▴ 300
135
votes
18
replies
158k
views
16 follow
Blast - Formatting Output
blast format output
updated 5 months ago by ▴ 20 • written 9.5 years ago by ▴ 320
134
votes
65
replies
3.9k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 20 hours ago by 39k • written 3.5 years ago by ▴ 880
134
votes
27
replies
41k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 13 months ago by 39k • written 11.1 years ago by 33k
131
votes
48
replies
14k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 11.8 years ago by ★ 2.6k • written 11.8 years ago by 11k
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 11 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
130
votes
37
replies
12k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 11.8 years ago by ★ 1.3k • written 11.8 years ago by ▴ 820
129
votes
22
replies
52k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 2 days ago by 85k • written 5.5 years ago by ★ 1.8k
129
votes
32
replies
123k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 14 months ago by 39k • written 12.3 years ago by ▴ 530
129
votes
38
replies
6.0k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 7 days ago by 39k • written 4.2 years ago by 98k
128
votes
83
replies
10k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
fastq compressor lossless fastq compression Tool
5.9 years ago by Petr Ponomarenko ★ 2.7k
127
votes
33
replies
56k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 7 months ago by 39k • written 9.1 years ago by ▴ 480
127
votes
19
replies
25k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq alignment next-gen R assembly
updated 2.2 years ago by 39k • written 3.7 years ago by ▴ 720
126
votes
24
replies
77k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 4.1 years ago by • 0 • written 10.0 years ago by ▴ 360
126
votes
19
replies
173k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 2.1 years ago by • 0 • written 11.0 years ago by ▴ 350
126
votes
44
replies
28k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 12 weeks ago by 39k • written 6.7 years ago by ▴ 970
125
votes
46
replies
44k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 8 weeks ago by 39k • written 7.3 years ago by ★ 3.2k
124
votes
29
replies
6.3k
views
18 follow
What License Do You Use When You Release Code And Data?
general software subjective
updated 9.5 years ago by 20 • written 13.2 years ago by 7.4k
122
votes
11
replies
161k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 21 months ago by • 0 • written 12.9 years ago by 4.9k
122
votes
42
replies
9.0k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 3 months ago by 39k • written 10.5 years ago by 98k
122
votes
17
replies
71k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 14 months ago by 39k • written 12.1 years ago by ▴ 370
121
votes
44
replies
19k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 3 months ago by 39k • written 13.0 years ago by 5.3k
120
votes
8
replies
78k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 17 months ago by 39k • written 8.7 years ago by ▴ 520
120
votes
53
replies
91k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 11 weeks ago by • 0 • written 9.0 years ago by ▴ 330
120
votes
33
replies
36k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 29 days ago by ★ 2.3k • written 9.8 years ago by 11k
119
votes
23
replies
28k
views
14 follow
Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
cram bam io hdf
updated 2.2 years ago by 39k • written 8.9 years ago by ▴ 320
119
votes
25
replies
119k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 6.3 years ago by ▴ 160 • written 12.9 years ago by 4.9k
118
votes
31
replies
180k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 20 months ago by 129k • written 13.2 years ago by 11k
118
votes
7
replies
108k
views
Bam And Indexed Bam Files
bam index
11.4 years ago by Sahel ▴ 260
118
votes
15
replies
102k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.4 years ago by • 0 • written 12.6 years ago by ▴ 210
118
votes
26
replies
33k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 12 weeks ago by ▴ 50 • written 8.0 years ago by ▴ 610
117
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 7 months ago by 129k • written 12.5 years ago by ★ 3.3k
117
votes
59
replies
30k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware next-gen
updated 4 months ago by 39k • written 8.1 years ago by ▴ 30
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 12 weeks ago by 39k • written 4.9 years ago by 72k
116
votes
35
replies
7.2k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 3 months ago by 39k • written 10.2 years ago by 21k
110,516 results • Page 2 of 2211
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: switching from illumination to NEB prep kits by GenoMax 129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by Zhichao • 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values by ATpoint 72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2 by ATpoint 72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts by ATpoint 72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by ATpoint 72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values by ATpoint 72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments by Alexander ▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
Thanks a lot, it works
Comment: Differential protein expression analysis by dsull ★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis by Ribo ▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
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