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3,236 results • Page 2 of 65
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26
votes
10
replies
3.7k
views
6 follow
Forum: Why not merging?
fastq sequencing
updated 22 days ago by 39k • written 5.9 years ago by 16k
26
votes
8
replies
1.3k
views
7 follow
Forum: Reasons to refuse to give support
design rna-seq statistics
updated 12 days ago by 39k • written 4.6 years ago by 8.3k
25
votes
22
replies
11k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 18 days ago by 39k • written 6.3 years ago by 18k
25
votes
7
replies
1.5k
views
6 follow
Forum: What Are The Best Bioinformatics Course Materials [2020]
course teaching
updated 18 days ago by 39k • written 2.5 years ago by 8.4k
24
votes
26
replies
1.8k
views
6 follow
Forum: Organizing a Bioinformatics Conference ?
meeting conference
updated 20 days ago by 39k • written 5.6 years ago by 154k
24
votes
21
replies
6.1k
views
9 follow
News: Misunderstood parameter of NCBI BLAST
blast alignment
updated 12 days ago by 39k • written 4.7 years ago by ★ 3.4k
23
votes
15
replies
4.2k
views
6 follow
Forum: On the usage of Golang
assembly next-gen alignment
updated 12 days ago by 39k • written 4.7 years ago by ▴ 80
23
votes
10
replies
2.4k
views
10 follow
Any suggestions for basic intro to submitting jobs to an HPC cluster?
ngs hpc
updated 13 days ago by 39k • written 4.8 years ago by ▴ 400
23
votes
41
replies
2.5k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS biopython illumina WGS
updated 27 days ago by 39k • written 7 weeks ago by ▴ 30
22
votes
11
replies
2.7k
views
Forum: ExpressionSet in the age of tidyverse
expressionset R bioconductor
updated 15 days ago by 39k • written 5.1 years ago by 13k
22
votes
15
replies
7.0k
views
11 follow
Forum: RNASeq user experience with Novogene?
RNA-Seq
updated 13 days ago by 39k • written 4.9 years ago by ▴ 80
22
votes
12
replies
1.5k
views
6 follow
Forum: What were the most impactful Bioinformatics papers published this year
papers publications
updated 18 hours ago by 39k • written 3.5 years ago by ▴ 510
21
votes
11
replies
1.6k
views
Forum: Most important International Big Data Projects: Genetics and Epigenetics
big-data
updated 13 days ago by 39k • written 4.8 years ago by ★ 9.3k
21
votes
11
replies
1.6k
views
8 follow
Forum: what I want to do after the PhD?
PhD
updated 26 days ago by 39k • written 6.2 years ago by ★ 4.2k
21
votes
15
replies
1.5k
views
9 follow
Forum: Working abroad without a PhD
career
updated 1 day ago by 39k • written 3.7 years ago by ★ 1.4k
20
votes
7
replies
2.8k
views
k-mer counting into R using perfect hashing
k-mer Rcpp Cpp hashing R
updated 15 days ago by 39k • written 7.0 years ago by ▴ 120
20
votes
24
replies
6.0k
views
6 follow
Forum: Python or R
RNA-Seq alignment next-gen-sequencing
updated 14 days ago by 39k • written 5.0 years ago by ▴ 160
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 20 days ago by 39k • written 5.5 years ago by ★ 3.4k
20
votes
19
replies
3.1k
views
7 follow
Bioinformatics word cloud to use in classes
teaching education
updated 11 days ago by 39k • written 4.3 years ago by ▴ 50
20
votes
6
replies
4.2k
views
Some clarification on enrichment analyses and pathway analyses?
pathview R gene-enrichment RNA-Seq
updated 20 days ago by 39k • written 5.6 years ago by ★ 1.5k
19
votes
9
replies
27k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis RNA-Seq ngs
updated 20 days ago by 39k • written 5.6 years ago by ▴ 500
19
votes
2
replies
3.1k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 26 days ago by 39k • written 6.2 years ago by ▴ 640
19
votes
9
replies
3.1k
views
Forum: How to self-study (get onto) Bioinformatics and Data Analysis for Genomic, for working with real life genomics data?
R genome RNA-Seq Python
updated 13 days ago by 39k • written 4.9 years ago by ▴ 720
19
votes
15
replies
1.3k
views
6 follow
Forum: Cross out line in Biostars
meta
updated 14 days ago by 39k • written 5.1 years ago by 5.3k
19
votes
6
replies
3.1k
views
Forum: ngs vs microarray
microarray ngs
updated 13 days ago by 39k • written 4.9 years ago by ▴ 20
19
votes
11
replies
1.5k
views
7 follow
Has anyone here worked with CNCI before? EXHAUSTED
software-error CNCI RNA-Seq
updated 1 day ago by 39k • written 3.7 years ago by ▴ 170
18
votes
6
replies
6.5k
views
VCF header line counting
vcf header
updated 11 days ago by ▴ 530 • written 8.3 years ago by ▴ 40
18
votes
7
replies
3.8k
views
Forum: Review of the CIGAR string format
alignment
updated 12 days ago by 39k • written 4.6 years ago by 7.9k
18
votes
4
replies
2.5k
views
Paternity Testing from WGS Trio
WGS trio paternity test DNA-Seq
updated 22 days ago by ▴ 330 • written 4.7 years ago by ▴ 50
18
votes
9
replies
2.9k
views
6 follow
Job: Seeking private tutor to learn RNA/ChIP-Seq data analysis
RNA-Seq ChIP-Seq
updated 25 days ago by 39k • written 6.1 years ago by ▴ 40
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 25 days ago by 39k • written 6.1 years ago by 5.2k
18
votes
11
replies
1.9k
views
8 follow
Forum: Create a File format to store Variant
hgvs json variant
updated 13 days ago by 39k • written 4.9 years ago by ★ 2.4k
18
votes
3
replies
5.5k
views
How to process (seems) Agilent microarrry data?
microarray rna
updated 10 days ago by • 0 • written 3.9 years ago by ★ 1.2k
18
votes
39
replies
3.0k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 15 days ago by 39k • written 4.2 years ago by ▴ 50
18
votes
12
replies
2.0k
views
6 follow
Forum: why GATK makes things more complicated ?
genomics
updated 11 days ago by 39k • written 4.3 years ago by ▴ 260
18
votes
2
replies
2.9k
views
Forum: Scripts on the Web: Bioinformatics Recipes
bioinformatics
updated 15 days ago by 39k • written 5.2 years ago by 98k
18
votes
16
replies
1.4k
views
Forum: Why are people not working on gene prioritization and candidate gene selection for new experiment design?
gene-prioritization
updated 12 days ago by 39k • written 4.7 years ago by ▴ 20
18
votes
9
replies
3.0k
views
MAPQ filtering for clinical applications
MAPQ clinical NGS
updated 14 days ago by ▴ 40 • written 5.7 years ago by 85k
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 26 days ago by 39k • written 6.2 years ago by 52k
17
votes
8
replies
5.1k
views
Applying Patches To Grch Assembly
assembly human freeze genome
updated 5 days ago by 21k • written 11.0 years ago by ★ 1.3k
17
votes
14
replies
1.5k
views
10 follow
Forum: What would be the trend in next few years in NGS era?
NGS sequencing
updated 12 days ago by 39k • written 4.6 years ago by ▴ 750
17
votes
17
replies
1.5k
views
6 follow
Forum: Journal for beginners
journal
updated 15 days ago by 39k • written 5.2 years ago by ▴ 20
16
votes
11
replies
3.3k
views
How to find out total # of CpGs sites from a fasta file?
sequence Cpp fasta CpG
updated 15 days ago by 39k • written 6.5 years ago by ▴ 60
16
votes
10
replies
2.0k
views
Forum: Asking for feedback on a Python library for computing alignments
alignment Python
updated 48 minutes ago by ▴ 70 • written 16 months ago by ▴ 60
16
votes
7
replies
1.0k
views
Forum: What counts as "complex code"?
career
updated 13 days ago by 39k • written 4.8 years ago by ▴ 30
16
votes
9
replies
9.7k
views
6 follow
problems with MAF for MutSigCV (vcf2maf)
vcf2maf snp vcf MutSigCV gatk
updated 9 days ago by • 0 • written 8.9 years ago by ★ 2.6k
16
votes
6
replies
6.9k
views
7 follow
Forum: What computer skills should I put on my resume?
resume genome
updated 19 days ago by 39k • written 5.5 years ago by ▴ 30
16
votes
10
replies
15k
views
Regarding Split reads and discordant reads
genome sequence sequencing alignment
updated 20 days ago by 39k • written 5.6 years ago by ▴ 50
16
votes
14
replies
2.7k
views
7 follow
Suggestions regarding bioinformatics journal
journal
updated 19 days ago by 39k • written 5.5 years ago by ★ 1.5k
15
votes
6
replies
3.5k
views
Forum: Which database software is better for bioinformatics web development? MySQL or MongoDB?
database mysql mongodb software
updated 13 days ago by 39k • written 4.7 years ago by ▴ 10
3,236 results • Page 2 of 65
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 Awards • All
Popular Question to lait ▴ 170
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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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