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418 results • Page 3 of 9
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18
votes
12
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2.5k
views
6 follow
Forum: why GATK makes things more complicated ?
genomics
updated 11 months ago by 43k • written 5.3 years ago by ▴ 280
6
votes
6
replies
2.5k
views
Forum: Trouble finding job with MS in Bioinformatics
next-gen
updated 11 months ago by 43k • written 6.0 years ago by ▴ 10
6
votes
4
replies
2.5k
views
Forum: Ru/Read Until in Nanopore sequencers
Oxford-Nanopore alignment sequencing
updated 11 months ago by 43k • written 4.2 years ago by ★ 1.7k
12
votes
14
replies
2.5k
views
8 follow
Forum: Recovering bam files after unknown deletion in the storage
photorec bam sequencing
written 4.9 years ago by ▴ 70
8
votes
6
replies
2.5k
views
Forum: How do you organize sequence data (FASTQs)?
RNA-Seq sequencing
updated 11 months ago by 43k • written 6.1 years ago by ▴ 280
11
votes
9
replies
2.5k
views
7 follow
Forum: Feature Selection and Dimensionality Reduction in 10X scRNA-seq data
software-error pca scRNA-seq
updated 12 months ago by 43k • written 4.4 years ago by 82k
8
votes
15
replies
2.4k
views
7 follow
Forum: How to identify your analytic data is true?
RNA-Seq ChIP-Seq next-gen-sequencing
updated 12 months ago by 43k • written 6.8 years ago by ▴ 80
18
votes
11
replies
2.4k
views
8 follow
Forum: Create a File format to store Variant
hgvs json variant
updated 11 months ago by 43k • written 5.9 years ago by ★ 2.4k
5
votes
5
replies
2.4k
views
Forum: BCL files as deliverables from a sequencing center
core-facility service-provider
updated 11 months ago by 43k • written 5.0 years ago by 5.2k
9
votes
14
replies
2.4k
views
Forum: MS Bioinformatics Project
assembly sequencing alignment R SNP
updated 11 months ago by 43k • written 6.1 years ago by ▴ 10
7
votes
8
replies
2.4k
views
Forum: Virus Genome Length and GC Content of SARS-COV-2 causing COVID-19
sequence genome
updated 11 months ago by 43k • written 4.1 years ago by ▴ 30
15
votes
10
replies
2.4k
views
6 follow
Forum: help identifying bioinformatics operations tools
database next-gen operations genomics
updated 11 months ago by 43k • written 5.5 years ago by ▴ 80
6
votes
5
replies
2.3k
views
Forum: Maintaning internal or private installation of Biostar or a similar Q&A site
Biostars
6 months ago by tshtatland ▴ 190
11
votes
9
replies
2.3k
views
Forum: Survey: help define Gencode and NCBI primary transcripts
refseq ensembl gencode ncbi transcript
updated 11 months ago by 43k • written 6.1 years ago by 23k
10
votes
7
replies
2.3k
views
Forum: How to learn bioinformatics?
learning
updated 3 months ago by ★ 1.3k • written 24 months ago by ▴ 20
28
votes
15
replies
2.3k
views
12 follow
Forum: Should bioinformaticians learn the scientific names of plants and animals?
sequence
updated 11 months ago by 43k • written 5.8 years ago by ▴ 10
6
votes
1
reply
2.3k
views
Forum: How to become employable in Bioinformatics, starting with degree and experience in CS/Software Engineering?
computer-scientist software-engineer
updated 11 months ago by 43k • written 5.8 years ago by • 0
30
votes
16
replies
2.3k
views
9 follow
Forum: Which programming langauge shall I start as a beginner in Bioinformatics
programming-language single-cell
updated 11 months ago by 43k • written 4.0 years ago by • 0
0
votes
1
reply
2.2k
views
Forum: How's the bioinformatics engineering path? How to become a bioinformatics engineer?
machine-learning Bioinformatics-engineer
updated 11 months ago by 43k • written 4.0 years ago by ▴ 70
4
votes
2
replies
2.2k
views
Forum: wet-lab vs dry-lab scientists
cv language
updated 11 months ago by 43k • written 4.3 years ago by 13k
0
votes
4
replies
2.2k
views
Forum: Multiple Sequence Alignment Applications
snp
updated 11 months ago by 43k • written 4.8 years ago by • 0
10
votes
6
replies
2.2k
views
Forum: How to acknowledge in the paper a reference genome that hasn't been published yet?
reference paper
updated 11 months ago by 43k • written 5.7 years ago by ▴ 140
31
votes
16
replies
2.2k
views
8 follow
Forum: What is in your opinion the current state-of-the-art sequencing platform for genomic assembly (Nov 2019)
next-gen-sequencing assembly genome
updated 11 months ago by 43k • written 4.5 years ago by ★ 5.1k
19
votes
14
replies
2.2k
views
Forum: What is the amount of sequencing data produced annually?
data research sequencing
updated 7 months ago by 22k • written 7 months ago by ▴ 70
15
votes
9
replies
2.2k
views
6 follow
Forum: [Opinion] - What alignment software do you use?
next-gen alignment
updated 11 months ago by 43k • written 6.1 years ago by ▴ 30
7
votes
4
replies
2.2k
views
Forum: How hard it is to get a bioinformatics degree in one country but find a career in another country?
career Masters
updated 11 months ago by 43k • written 5.9 years ago by ▴ 10
1
vote
6
replies
2.2k
views
Forum: shotgun sequencing and clone-based sequencing
sanger-sequencing
updated 12 months ago by 43k • written 6.7 years ago by • 0
26
votes
27
replies
2.2k
views
10 follow
Forum: Determining computer time required
computer hpc time
updated 3 months ago by ★ 6.0k • written 4 months ago by ▴ 40
14
votes
10
replies
2.2k
views
Forum: WGBS alignment with BitMapperBS
BitMapperBS bismark
updated 11 months ago by 43k • written 4.8 years ago by ★ 9.4k
10
votes
15
replies
2.2k
views
Forum: How should reference genome fasta files be distributed by UCSC?
reference-genome fasta freeze ucsc-genome-browser
updated 11 months ago by 22k • written 14 months ago by ★ 1.6k
3
votes
6
replies
2.2k
views
Forum: Choosing the appropriate test for differential analysis: Limma or Mann-Whitney (with BH correction)? Test for normality
R Shapiro-Wilk Limma Mann-Whitney
updated 11 months ago by 43k • written 4.0 years ago by ▴ 40
24
votes
26
replies
2.1k
views
6 follow
Forum: Organizing a Bioinformatics Conference ?
meeting conference
updated 12 months ago by 43k • written 6.5 years ago by 161k
3
votes
14
replies
2.1k
views
6 follow
Forum: Search for gene variants
next-gen
updated 11 months ago by 43k • written 5.7 years ago by 8.3k
16
votes
8
replies
2.1k
views
8 follow
Forum: What are the most important unresolved problems in Bioinformatics?
bioinformatics
updated 10 months ago by 43k • written 7.6 years ago by ★ 2.5k
21
votes
15
replies
2.1k
views
9 follow
Forum: Working abroad without a PhD
career
updated 11 months ago by 43k • written 4.6 years ago by ★ 1.4k
49
votes
20
replies
2.1k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 4 months ago by ★ 2.6k • written 4 months ago by ★ 27k
7
votes
20
replies
2.1k
views
Forum: NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR RNA-Seq TopHat
updated 12 months ago by 43k • written 3.3 years ago by ▴ 10
0
votes
6
replies
2.1k
views
7 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers
software-error
updated 11 months ago by 43k • written 5.7 years ago by • 0
1
vote
8
replies
2.1k
views
Forum: Memory-driven computing accelerates genomic data processing
HPC
updated 11 months ago by 43k • written 5.3 years ago by 11k
23
votes
11
replies
2.1k
views
9 follow
Forum: file and directory management best practices
file-management
updated 11 months ago by 43k • written 3.7 years ago by ▴ 140
0
votes
0
replies
2.1k
views
Forum: Genetic linkage analysis software tools and comparison
genetic linkage-analysis
updated 12 months ago by 43k • written 6.7 years ago by ★ 9.4k
19
votes
15
replies
2.0k
views
6 follow
Forum: Cross out line in Biostars
meta
updated 11 months ago by 43k • written 6.0 years ago by 5.3k
21
votes
11
replies
2.0k
views
Forum: Most important International Big Data Projects: Genetics and Epigenetics
big-data
updated 11 months ago by 43k • written 5.8 years ago by ★ 9.4k
10
votes
7
replies
2.0k
views
Forum: Is trimming always better?
RNA-Seq QC trimmomatic trimming
updated 11 months ago by 43k • written 4.9 years ago by ▴ 330
5
votes
8
replies
2.0k
views
7 follow
Forum: Ranking of Bioinformatics tools & resources by the number of users
bioinformatics-tools
updated 11 months ago by 43k • written 5.7 years ago by ▴ 40
7
votes
4
replies
2.0k
views
Forum: Bioinformatics / Computational Biology PhD
Computational-Biology bioinformatics PhD
updated 10 months ago by 43k • written 8.2 years ago by • 0
7
votes
8
replies
2.0k
views
Forum: Would solving many Rosalind problems show your ability for this field in job-wise?
rosalind career
11 months ago by K • 0
3
votes
6
replies
2.0k
views
Forum: Are you using GATK ?
GATK4 GATK
updated 12 months ago by 43k • written 6.6 years ago by ▴ 20
17
votes
17
replies
2.0k
views
6 follow
Forum: Journal for beginners
journal
updated 11 months ago by 43k • written 6.1 years ago by ▴ 20
23
votes
12
replies
2.0k
views
6 follow
Forum: Whole-Exome Analysis on a Mainstream Desktop PC
NGS whole-exome
updated 11 months ago by 43k • written 3.9 years ago by 11k
418 results • Page 3 of 9
Recent Votes
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
Split multiallelic SNPs to biallelic from vcf
Filtering multi-allelic sites in VCF files
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Recent Replies
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by GenoMax 142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file by ramiro.barrantes • 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content by ntsopoul ▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content by ATpoint 82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object by ATpoint 82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments? by J. ▴ 40
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs? by GenoMax 142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs? by i.sudbery 19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq by ATpoint 82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
Comment: Biomart issue, why so few 3'utrs? by i.sudbery 19k
Which species is this?
Comment: How to access GWAVA software of data by GenoMax 142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
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