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3
votes
3
replies
304
views
Forum: [Meta] Use of AI
Artificial ChatGPT Intelligence Biostars AI
updated 19 hours ago by 129k • written 1 day ago by ★ 2.9k
2
votes
2
replies
178
views
Forum: Colleges
Colleges india universities
updated 4 days ago by 39k • written 5 days ago by • 0
10
votes
15
replies
1.0k
views
Forum: How should reference genome fasta files be distributed by UCSC?
reference-genome fasta freeze ucsc-genome-browser
updated 3 days ago by 21k • written 3 months ago by ★ 1.5k
1.2k
votes
206
replies
50k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 4 days ago by ★ 1.2k • written 12.2 years ago by 21k
12
votes
2
replies
2.6k
views
Forum: List of genome annotation tools (>140)
gene genome
updated 2 days ago by 39k • written 3.8 years ago by 7.9k
10
votes
7
replies
1.4k
views
Forum: Is trimming always better?
RNA-Seq QC trimmomatic trimming
updated 4 days ago by 39k • written 3.9 years ago by ▴ 330
14
votes
11
replies
5.4k
views
7 follow
Forum: Do you need a deduplication tool for FASTQ data in fastp?
deduplication fastp
updated 4 days ago by 39k • written 4.0 years ago by ★ 2.4k
11
votes
7
replies
5.1k
views
Forum: Using Graphics Processing Units (GPUs) in bioinformatics
algorithm GPU
updated 2 days ago by 39k • written 3.8 years ago by ▴ 270
4
votes
3
replies
724
views
Forum: When to ask for rerun from vendors
ngs-vendor
updated 2 days ago by 39k • written 3.7 years ago by ★ 1.9k
13
votes
4
replies
983
views
Forum: The shortcoming of shiny app in building webserver
R shiny webserver
updated 2 days ago by 39k • written 3.7 years ago by ▴ 110
1
vote
3
replies
722
views
Forum: The pStacks module of Stacks has been removed?
software-error
updated 2 days ago by 39k • written 3.8 years ago by ▴ 20
3
votes
3
replies
905
views
Forum: Large Multi-omics Project -- Dev Approach
snp RNA-Seq sequencing
updated 2 days ago by 39k • written 3.8 years ago by ▴ 10
12
votes
4
replies
1.3k
views
Forum: Bioinformatics and biotechnology market in future.
genome next-gen
updated 2 days ago by 39k • written 3.8 years ago by • 0
3
votes
0
replies
879
views
Forum: Good books on application of Machine Learning in Bioinformatics
book machine-learning
updated 2 days ago by 39k • written 3.8 years ago by ▴ 180
0
votes
2
replies
1.1k
views
Forum: What should I choose between a thesis and a project for masters in bioinformatics?
thesis project
updated 2 days ago by 39k • written 3.8 years ago by ▴ 70
4
votes
0
replies
913
views
Forum: Plotting Ensembl gene name changes between versions
R ensembl
updated 2 days ago by 39k • written 3.8 years ago by ▴ 550
1
vote
2
replies
804
views
Forum: What Are The Big Problems/Current Trends In Proteomics?
proteomics sequencing
updated 3 days ago by 39k • written 3.9 years ago by • 0
0
votes
4
replies
1.7k
views
Forum: Multiple Sequence Alignment Applications
snp
updated 3 days ago by 39k • written 3.9 years ago by • 0
4
votes
13
replies
1.3k
views
Forum: Looking for Participants: Meenta NovaSeq RunShare Beta
RunShare next-gen NovaSeq
updated 3 days ago by 39k • written 3.9 years ago by ▴ 10
14
votes
10
replies
1.6k
views
Forum: WGBS alignment with BitMapperBS
BitMapperBS bismark
updated 3 days ago by 39k • written 3.9 years ago by ★ 9.3k
13
votes
6
replies
937
views
Forum: To Cloud or Not to Cloud - Privacy implications of genetic data sharing
security diagnostics DNA-Seq
updated 5 days ago by 39k • written 3.9 years ago by 9.9k
0
votes
1
reply
745
views
Forum: Tools and data for plant proteins
alignment sequencing
updated 4 days ago by 39k • written 3.9 years ago by • 0
14
votes
5
replies
6.1k
views
Forum: Seurat vs Monocle
R RNA-Seq next-gen single-cell
updated 3 days ago by 39k • written 3.9 years ago by 3.2k
5
votes
3
replies
711
views
Forum: price of MSI detection by NGS for 1 person
next-gen
updated 4 days ago by 39k • written 3.9 years ago by ▴ 20
3
votes
2
replies
604
views
Forum: Application suggestions for slackbot
slack
updated 4 days ago by 39k • written 4.0 years ago by ★ 2.1k
11
votes
13
replies
3.5k
views
6 follow
Forum: NGS Data storage solutions for small organisations or big labs
big-data HTS storage NGS metagenomics
updated 4 days ago by 39k • written 4.0 years ago by ▴ 830
1
vote
5
replies
1.2k
views
Forum: PhD: Research interest or better program?
PhD
updated 4 days ago by 39k • written 4.0 years ago by • 0
11
votes
5
replies
4.2k
views
Forum: Bioinformatics Workstation Suggestions
RNA-Seq next-gen workstation
updated 4 days ago by 39k • written 4.0 years ago by ▴ 90
12
votes
13
replies
1.8k
views
6 follow
Forum: Recovering bam files after unknown deletion in the storage
photorec bam sequencing
updated 4 days ago by 39k • written 4.0 years ago by ▴ 70
1
vote
1
reply
941
views
Forum: Companies and salary for a PhD in Drug Design in Asia
salary drug-design
updated 4 days ago by 39k • written 4.0 years ago by • 0
1
vote
1
reply
1.5k
views
Forum: Free Bioinformatics Training Resources (for non-bioinformaticians)
RNA-Seq
updated 4 days ago by 39k • written 4.0 years ago by ▴ 340
4
votes
4
replies
1.4k
views
Forum: When will the hg19/grch37 finally become obsolete?
Reference-Genome
updated 4 days ago by 39k • written 4.0 years ago by ▴ 10
3
votes
1
reply
826
views
Forum: Recommend papers: automated vs manual downstream analysis
downstream-analysis reproducibility
updated 4 days ago by 39k • written 4.1 years ago by ▴ 110
0
votes
0
replies
615
views
Forum: Survey for job context
survey interview
updated 4 days ago by 39k • written 4.0 years ago by • 0
4
votes
0
replies
3.3k
views
Forum: How can unique molecular identifiers (UMIs) help to reduce quantitative biases?
NGS Variant-Calling Unique-Molecular-Identifier
updated 4 days ago by 39k • written 4.0 years ago by 9.9k
11
votes
5
replies
1.2k
views
Forum: What bioinformatic training?
training RNA-Seq illumina
updated 4 days ago by 39k • written 4.0 years ago by ▴ 150
5
votes
5
replies
2.0k
views
Forum: BCL files as deliverables from a sequencing center
core-facility service-provider
updated 4 days ago by 39k • written 4.0 years ago by 5.2k
4
votes
4
replies
987
views
Forum: What skills are required for an informatics scientist?
informatics scientist
updated 4 days ago by 39k • written 4.0 years ago by ★ 9.3k
0
votes
1
reply
805
views
Forum: An idea for a project in ML
ML matlab machine-learning data-science
updated 4 days ago by 39k • written 4.0 years ago by • 0
10
votes
4
replies
5.3k
views
Forum: Bioinformatics: Which language should I learn
programming
updated 5 days ago by 39k • written 4.1 years ago by • 0
3
votes
7
replies
764
views
Forum: Construct a small computing server for GWAS Analysis
assembly
updated 5 days ago by 39k • written 4.1 years ago by ▴ 60
1
vote
1
reply
536
views
Forum: Whither my badges?
meta
updated 5 days ago by 39k • written 4.1 years ago by ★ 1.9k
2
votes
3
replies
663
views
Forum: What are the major types of choices that affect an analysis?
reproducibility
updated 5 days ago by 39k • written 4.1 years ago by 21k
5
votes
2
replies
1.0k
views
Forum: ISMB bioinfo-core workshop call for lightning talks
conferences
updated 5 days ago by 39k • written 4.1 years ago by 5.3k
7
votes
9
replies
1.2k
views
Forum: 10 Most important topic in Human evolutionary genomics
evolutionary-genomics evolutionary-medicine
updated 5 days ago by 39k • written 4.2 years ago by ▴ 40
113
votes
53
replies
5.2k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 5 days ago by 39k • written 4.2 years ago by ▴ 170
1
vote
3
replies
825
views
Forum: Poorly designed "omics" experiment
RNA-Seq next-gen ChIP-Seq
updated 5 days ago by 39k • written 4.2 years ago by ▴ 100
129
votes
38
replies
5.9k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 5 days ago by 39k • written 4.2 years ago by 98k
1
vote
2
replies
1.1k
views
Forum: GENEWIZ RNA-seq quality feedback
RNA-Seq QC sequencing
updated 5 days ago by 39k • written 4.2 years ago by ▴ 20
1
vote
2
replies
839
views
Forum: Homologous sequences problematic in RNA-seq
Homology genome RNA-Seq
updated 5 days ago by 39k • written 4.2 years ago by ▴ 10
52 results • Page 1 of 2
Recent Votes
Answer: How to sort gff3 according to chromosome order?
Answer: how to sort unique seq from fasta files
Answer: Make a BedGraph file
Answer: Finding Enhancers using Genomation library
A: Extracting N positions from fasta file
Comment: Gene enrichment analysis
Comment: Gene enrichment analysis
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Recent Replies
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file by kirillkirilenko ▴ 10
It works, thank you!
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by Cathal • 0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
Answer: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
genomation is based on GenomicRanges which uses 1-based coordinates. https://www.biostars.org/p/84686/ Since a single CpG has a length o…
Comment: Gene enrichment analysis by ATpoint 72k
I cannot speak for this package but I recommend clusterProfiler where the universe argument isindeed all tested genes so your background.
Answer: Finding Enhancers using Genomation library by ATpoint 72k
You cannot derive enhancers from methylation profiles. Enhancers are regulatory elements, and they either are methylated or not. There is l…
Answer: convert data frame with character column to data frame with integer column by Basti ★ 1.5k
Cross-posted and answered there : https://stackoverflow.com/questions/76388032/convert-data-frame-with-character-column-to-data-frame-with-…
Comment: Getting same value for start and end position, "DNA methylation" by Basti ★ 1.5k
Your question lacks precision, we do not know what you are talking about
Comment: Gene enrichment analysis by Meisam ▴ 180
If you want to find enrichment of your selected genes versus the superset of all genes detected, then yes you mean the background. And to d…
Comment: WGCNA Trait File Issues by LChart 2.6k
The NAs are coming from the fact that each 'Sample' (which I assume is a unique identifier for a sample) is not actually a number and so th…
Answer: Why is coordinate sort required before findng read depths? by zhang yi xing ▴ 10
hi ,you can look at this fig in software **mosdepth** . By traversing a sorted BAM file from the beginning, one can obtain depth informat…
Comment: Getting species names and taxa id from assembly accession number by Mensur Dlakic ★ 23k
You should probably not advertise your personal email. It is not needed to understand the code. I don't know what exactly is the problem w…
Answer: how to sort unique seq from fasta files by shenwei356 8.1k
[seqkit common](https://bioinf.shenwei.me/seqkit/usage/#common) finds common sequences of multiple files by id/name/sequence seqkit co…
Answer: how to sort unique seq from fasta files by Mensur Dlakic ★ 23k
[**CD-HIT**][1] will remove all sequences that share identity above a certain threshold. If you set that threshold at `1.0` (meaning 100% i…
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