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5
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4
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1.4k
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Forum: Best BAM viewer in 2022
sam bam
updated 10 months ago by 43k • written 17 months ago by ▴ 70
1.2k
votes
206
replies
60k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 11 months ago by ★ 1.4k • written 13.1 years ago by 22k
15
votes
13
replies
4.2k
views
8 follow
Forum: Does a PhD or work experience set you up better to do bioinformatics work in industry?
advice industry phd
updated 3 months ago by 3.9k • written 18 months ago by ▴ 30
0
votes
2
replies
993
views
Forum: Best Phd Programs in Usa ( Computational Biology)
computational-biology drug-design
updated 17 months ago by 43k • written 19 months ago by • 0
4
votes
5
replies
1.4k
views
6 follow
Forum: Which Bioinformatics Master's degree is better?
career masters
updated 11 months ago by 43k • written 18 months ago by • 0
2
votes
1
reply
875
views
Forum: Package is not available (for R version XXX)？ Manually download and install R packages
installation package R
updated 16 months ago by 6.4k • written 18 months ago by ▴ 30
3
votes
6
replies
1.1k
views
Forum: How to become a moderator and other ways of contributing to Biostars
meta biostars
updated 11 months ago by 43k • written 19 months ago by 6.2k
2
votes
3
replies
953
views
Forum: Experiences with different cloud computing resources / providers
cloud pipeline rna-seq alignment
updated 20 months ago by 22k • written 20 months ago by ▴ 10
19
votes
13
replies
2.7k
views
8 follow
Forum: Can bioinformatics Phds be completely or almost completely done remotely?
PhD
updated 20 months ago by 6.5k • written 20 months ago by ▴ 40
8
votes
13
replies
2.9k
views
8 follow
Forum: Commercial software for genomics / NGS / bioinformatics
NGS software genomics
updated 20 months ago by • 0 • written 20 months ago by ★ 1.4k
4
votes
4
replies
1.4k
views
Forum: Bioinformatics analogies
Bioinformatics
updated 20 months ago by 100k • written 20 months ago by ▴ 70
2
votes
4
replies
1.2k
views
Forum: Is low N in-vivo research a blind spot for RNA-seq?
statistics metascience power sample-size
updated 13 months ago by 43k • written 20 months ago by ▴ 230
2
votes
4
replies
1.0k
views
Forum: strand specific data
strand DNA RNA specific coding
20 months ago by upasana • 0
3
votes
0
replies
827
views
Forum: Let's build a list of Drug Databases including Tyrosine Kinase Inhibitors: Update 1
pharmacology RTK IC50 TKI database
21 months ago by LauferVA 4.2k
7
votes
14
replies
2.4k
views
7 follow
Forum: Why isn't GWAS used in oncology?
gwas association oncology studies somatic cancer
updated 21 months ago by 3.9k • written 21 months ago by ▴ 90
4
votes
4
replies
1.4k
views
Forum: Cloud Computing Services available?
resources Cloud-Computing
updated 17 months ago by 43k • written 22 months ago by ★ 2.5k
2
votes
7
replies
1.3k
views
Forum: Build a Visual Analytic App for Rna-seq data [Ideas Accepted]
R plot rna-seq count
updated 21 months ago by 43k • written 21 months ago by ▴ 20
6
votes
3
replies
2.3k
views
Forum: Best formats for storing large amounts of data for random access
file-formats databases
updated 21 months ago by 4.6k • written 21 months ago by 19k
0
votes
1
reply
636
views
Forum: Add an intercept column to a bed file
plink intercept bed
updated 22 months ago by 82k • written 22 months ago by • 0
4
votes
2
replies
1.9k
views
Forum: Best resource for getting a person with a Math/Comp Sci background the right amount of Biology knowledge
biology teaching
updated 17 months ago by 43k • written 22 months ago by 4.2k
0
votes
0
replies
753
views
Forum: Normalization of ChIP-seq _ Spikein normalization + RPGC
ChIP-seq normalization RPGC Spikein Normalization
22 months ago by goddy93 • 0
3
votes
1
reply
701
views
Forum: Would an automated NGS analytics platform help research?
ngs data-analysis
updated 22 months ago by 43k • written 22 months ago by • 0
5
votes
2
replies
1.7k
views
Forum: Skills for industry career in bioinformatics
industry
updated 22 months ago by 13k • written 22 months ago by ▴ 10
9
votes
6
replies
1.3k
views
Forum: Programming languages in industry
programming language
updated 22 months ago by 9.7k • written 22 months ago by ▴ 30
2
votes
6
replies
1.3k
views
Forum: Getting the best of RNA-Seq
RNA-Seq isoform gene expression
22 months ago by Antonio R. Franco ★ 5.1k
1
vote
0
replies
807
views
Forum: Not all Over Representation Analyses are the same!
clusterProfiler Analysis fisher hypergeometric ORA Pathway
23 months ago by Francesco ▴ 20
3
votes
2
replies
860
views
Forum: From protein-protein interaction networks to..
workflow computational knowledge limitations
updated 11 months ago by 43k • written 23 months ago by ▴ 50
0
votes
0
replies
759
views
Forum: Best practices for merging vcfs with different positions + different samples?
vcf bcftools genotypes
updated 17 months ago by 43k • written 23 months ago by ▴ 30
24
votes
6
replies
5.0k
views
6 follow
Forum: Awk in Bioinformatics
perl awk shell
updated 17 months ago by 43k • written 5.7 years ago by ★ 9.4k
7
votes
8
replies
1.6k
views
Forum: Can we lock posts related to merging vcf files?
vcf
updated 17 months ago by 43k • written 23 months ago by 2.8k
0
votes
0
replies
651
views
Forum: Bioinformatics for understanding cancer and other diseases
cancer omics
updated 17 months ago by 43k • written 23 months ago by ★ 1.5k
1
vote
3
replies
2.5k
views
Forum: What counts as a valid biological replicate in single cell RNAseq?
statistics biological replicates scRNA-seq
updated 23 months ago by 3.9k • written 23 months ago by • 0
3
votes
3
replies
952
views
Forum: Looking for a PostDoc position in ML-heavy medical bioinformatics in Germany
Germany PostDoc
updated 23 months ago by 27k • written 23 months ago by ★ 2.9k
0
votes
0
replies
379
views
Forum: Can Bioinformatics be used in developing a product?
product company business
updated 17 months ago by 43k • written 23 months ago by ▴ 20
0
votes
2
replies
1.2k
views
Forum: Bioinformatics algorithm tutorials in C++/C
protein gene genome
updated 23 months ago by 54k • written 23 months ago by ▴ 980
34
votes
11
replies
9.4k
views
13 follow
Forum: Gallery: Computational tools for DNA methylation
computational-tools methylation
updated 21 months ago by 43k • written 8.5 years ago by ★ 9.4k
6
votes
8
replies
3.1k
views
Forum: PC build for Nanopore data analysis
python PC pipeline nanopore-sequencing
23 months ago by stan.aanhane ▴ 30
2
votes
3
replies
947
views
Forum: What is difference between Bioinformatics and Data Science?
Data-Science
updated 17 months ago by 43k • written 24 months ago by ▴ 30
2
votes
2
replies
951
views
Forum: Project ideas
project-ideas
updated 24 months ago by 54k • written 24 months ago by • 0
0
votes
0
replies
585
views
Forum: Beagle5 imputation accuracy
beagle5 DR2 imputation impute2 impute-info
2.0 years ago by ch333 • 0
1
vote
6
replies
1.1k
views
Forum: Bioinformatics Software Developer job interview steps and what to expect?
interview software-development
updated 22 months ago by 43k • written 2.0 years ago by • 0
2
votes
2
replies
793
views
Forum: What sequencing method is the most efficient for identifying genes driving rare diseases?
NGS GWAS WGS
updated 17 months ago by 43k • written 2.0 years ago by • 0
5
votes
5
replies
1.1k
views
Forum: Best book introducing R programming?
coding R
2.0 years ago by Scottie ▴ 10
4
votes
6
replies
1.6k
views
Forum: How relevant are read numbers in FastQ headers for paired reads?
header fastq number read
2.0 years ago by Matthias Zepper 4.6k
0
votes
0
replies
628
views
Forum: commonly-used bioinformatics pipeline
Galaxy
updated 17 months ago by 43k • written 2.0 years ago by ▴ 120
0
votes
0
replies
570
views
Forum: Master's topic in Bioinformatics
Bio-informatique
2.0 years ago by Badji Oumar • 0
13
votes
15
replies
3.4k
views
8 follow
Forum: Biostar under spam attack - restrictions added to post content and title
meta biostars
updated 15 months ago by 43k • written 8.9 years ago by 100k
0
votes
1
reply
803
views
Forum: Retrieve SCCM data for client software distribution serviceNow
training servicenow online
2.0 years ago by hkrtrainings408 • 0
47
votes
24
replies
6.5k
views
15 follow
Forum: What's fascinating about Bioinformatics for potential students?
career msc
updated 17 months ago by 43k • written 6.6 years ago by 54k
5
votes
8
replies
2.8k
views
Forum: SQL-why do we need it in Bioinformatics ?
SQL Programming
updated 17 months ago by 43k • written 2.1 years ago by ▴ 10
1,000 results • Page 3 of 20
Recent Votes
Answer: joint callset and vcf sorting, unknown TAG issue
Answer: joint callset and vcf sorting, unknown TAG issue
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
Gff To Vcf
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
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Recent Awards • All
Scholar to pjb39 ▴ 200
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Recent Replies
Answer: Practical Haplotype Graph v2 not finding correct paths by pjb39 ▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty by Mathew ▴ 90
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2 by BioinfGuru ★ 1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
Comment: Output file of satools flagstat empty by GenoMax 142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.
Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100
@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=0,Type=Flag,…
Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…
Comment: Tophat multiple or unique mapping criteria by Ruqaiya • 0
> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…
Comment: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k
> Still, I can't understand the Invalid tag name: "1000gALT" the following line is missing in the VCF header: ##INFO=<ID=1000gALT,Num…
Answer: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k
INFO at 121387974 is .;CpG this is an invalid INFO column. There is an invalid attribute named '.' followed by the attribute CpG, …
Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100
@Pierre Lindenbaum as I don't know the meaning of `.;` and I've seen there are many in both files, I simply removed them with `grep -v`. …
Comment: joint callset and vcf sorting, unknown TAG issue by Matteo Ungaro ▴ 100
My bad I switched positions between the two files when looking the first time. They do indeed look abnormal but how can I fix it? Below the…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py by beginner123 • 0
Hi, no I'm using the python implementation as linked above.
Comment: joint callset and vcf sorting, unknown TAG issue by Pierre Lindenbaum 161k
Show us the content of the INFO column at the problematic positions.
Comment: Tissue-specific DEG analysis with DEseq2 by ATpoint 82k
Sounds like full confounding. Be careful. Personally I would not do this comparison. There is no way to distinguish tissue effect from dono…
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