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1,000 results • Page 4 of 20
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27
votes
27
replies
29k
views
10 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 8 months ago by ▴ 240 • written 11.7 years ago by ★ 1.7k
132
votes
27
replies
40k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 11 months ago by 38k • written 11.0 years ago by 33k
42
votes
27
replies
4.4k
views
12 follow
What Do You Think Microsoft Biology Foundation?
updated 5 months ago by 38k • written 11.9 years ago by ▴ 820
53
votes
27
replies
3.5k
views
11 follow
Should General Programming Questions Actually Be Posted To Biostar?
meta biostars
updated 6 weeks ago by 38k • written 11.7 years ago by ★ 1.6k
63
votes
27
replies
26k
views
18 follow
Data Too Big To Be Stored In Memory: Common Options
python
updated 4 weeks ago by 38k • written 10.4 years ago by ▴ 720
294
votes
27
replies
41k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 8 months ago by 38k • written 7.2 years ago by ★ 2.4k
17
votes
26
replies
1.4k
views
File conversion in bash, discrepancy in number of lines after conversion.
bash
updated 7 days ago by 38k • written 2.9 years ago by ▴ 380
12
votes
26
replies
29k
views
getting intersect between two lists of genes in R
gene R
updated 8 months ago by 38k • written 7.4 years ago by ★ 4.1k
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 6 weeks ago by 38k • written 11.2 years ago by ▴ 300
118
votes
26
replies
32k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 19 days ago by ▴ 30 • written 7.9 years ago by ▴ 610
38
votes
26
replies
10.0k
views
Remove optical duplicates from bam file
sequencing
updated 8 months ago by 38k • written 8.5 years ago by ▴ 510
24
votes
26
replies
2.5k
views
Tool: ClinCNV: CNV detection from short reads
cnv calling cna Tool variant
9 months ago by German.M.Demidov ★ 2.9k
6
votes
26
replies
7.5k
views
Realign BAM files to other reference file
bam samtools
updated 7 days ago by 38k • written 4.7 years ago by ▴ 670
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 15 days ago by 38k • written 5.5 years ago by 84k
4
votes
26
replies
15k
views
10 follow
ADMIXTURE and R, color meaning on barplot in studing population ancestry, K value
R gene
updated 7 weeks ago by • 0 • written 7.6 years ago by ▴ 20
8
votes
26
replies
3.6k
views
Fasta sequence replacement based on header name
alignment Assembly sequencing RNA-Seq
updated 3 months ago by 38k • written 7.7 years ago by ★ 1.8k
9
votes
26
replies
7.6k
views
GREP: out of memory
Deseq2 macOS gff HEloci
updated 12 days ago by 38k • written 4.7 years ago by ▴ 110
171
votes
26
replies
6.8k
views
12 follow
How Do You Acknowledge Biostar And Its Contributors In Your Research Output?
meta biostars
updated 6 weeks ago by 38k • written 12.1 years ago by 3.2k
5
votes
26
replies
6.0k
views
Pre-computed list of genes in LD with a SNP with r2 from 1000Genomes / hg19
genomics snp ld
updated 3 months ago by 38k • written 8.6 years ago by 18k
20
votes
26
replies
5.0k
views
9 follow
Is there a better tool for visualizing your variants after annotation than Excel?
annotations variants
updated 7 months ago by 153k • written 5.1 years ago by ▴ 160
31
votes
26
replies
8.0k
views
12 follow
How To Discard Sequences Longer Than N Nucleotides ?
small rna data
updated 6 months ago by 38k • written 10.2 years ago by ▴ 110
37
votes
26
replies
3.9k
views
7 follow
Ngs Challenge: Can You Give An Insight About This Imaginary Genetic Disease ?
next-gen-sequencing
updated 6 weeks ago by 38k • written 11.3 years ago by 153k
16
votes
26
replies
14k
views
16 follow
bedtools coverage gives error received illegal bin number, but that number isn't in my data!
ChIP-Seq bedtools
updated 9 weeks ago by 38k • written 6.1 years ago by ▴ 30
65
votes
26
replies
18k
views
13 follow
Forum: Macosx For Bioinformatics?
linux
updated 28 days ago by 38k • written 9.3 years ago by 11k
26
votes
26
replies
3.3k
views
Are my RNA-seq datasets strand-specific?
alignment next-gen-sequencing RNA-Seq
updated 8 months ago by 38k • written 7.1 years ago by ★ 4.1k
105
votes
26
replies
38k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 6 months ago by 38k • written 10.2 years ago by ▴ 810
6
votes
26
replies
4.2k
views
6 follow
Is there a limit for SAMTOOLS tview option?
alignment
updated 7 months ago by ▴ 130 • written 5.4 years ago by ▴ 60
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 16 days ago by 38k • written 4.1 years ago by 16k
15
votes
26
replies
4.5k
views
How to interpret the result of GO analysis using Ontologizer / mapping GO IDs to GO TERMS ?
gene-ontology R RNA-Seq
updated 11 months ago by 38k • written 8.2 years ago by ▴ 960
25
votes
26
replies
3.0k
views
warning in R
R
updated 11 weeks ago by 38k • written 7.8 years ago by ★ 4.1k
34
votes
26
replies
14k
views
13 follow
Reliable Fastq compression programs
fastq compression reliability
updated 4 months ago by ▴ 250 • written 7.4 years ago by 11k
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 27 days ago by 38k • written 9.1 years ago by 97k
73
votes
25
replies
98k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 9 months ago by 38k • written 7.9 years ago by ▴ 250
7
votes
25
replies
9.4k
views
6 follow
Tool: MIGEC: towards error-free profiling of immune repertoires
sequencing-error tcr molecular-barcode antibody Tool
updated 5 months ago by 38k • written 8.9 years ago by 3.5k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 5 weeks ago by 38k • written 10.5 years ago by 97k
136
votes
25
replies
75k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 months ago by 38k • written 10.9 years ago by ★ 4.2k
69
votes
25
replies
6.2k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 6 weeks ago by 38k • written 13.0 years ago by ▴ 190
13
votes
25
replies
10k
views
9 follow
Tool: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
ngs analysis sequencing software Tool
updated 8 months ago by 38k • written 9.6 years ago by 3.5k
18
votes
25
replies
11k
views
6 follow
Extracting features or gene from PCA after calculating PCA for downstream analysis
R
9 months ago by krushnach80 ★ 1.1k
8
votes
25
replies
1.9k
views
construction of a database
sql noSQL neo4j database
updated 8 days ago by 38k • written 22 months ago by ▴ 20
11
votes
25
replies
5.0k
views
15 follow
News: Questions for the NCBI Next Generation Sequencing Online Workshop Can be Posted with the NCBI_NOW Tag
NCBI_NOW News
updated 6 months ago by 38k • written 7.5 years ago by ▴ 320
45
votes
25
replies
2.8k
views
9 follow
Blog: Evolution of Biostars
meta Biostars
updated 6 weeks ago by 38k • written 4.1 years ago by 7.0k
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 16 days ago by 2.6k • written 10.8 years ago by ▴ 820
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 12 days ago by 38k • written 6.7 years ago by ★ 9.3k
12
votes
25
replies
1.3k
views
Transform Data into DNA picture
DNA
updated 3 months ago by 47k • written 3 months ago by ▴ 120
111
votes
25
replies
64k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 7 weeks ago by ▴ 10 • written 12.2 years ago by 153k
15
votes
25
replies
1.8k
views
6 follow
Forum: How to get help on a question that has been buried?
meta biostars
updated 6 weeks ago by 38k • written 7.0 years ago by ▴ 710
91
votes
25
replies
57k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 6 months ago by 52k • written 12.1 years ago by 3.4k
17
votes
25
replies
4.8k
views
Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
metatranscriptomics RNA-Seq Illumina
updated 9 months ago by 38k • written 8.0 years ago by ▴ 650
23
votes
25
replies
2.2k
views
bash and awk code
bash awk terminal
3 months ago by Sam ▴ 150
1,000 results • Page 4 of 20
Recent Votes
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
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Recent Replies
Answer: Any tips in landing a bioinformatic job? by Vincent Laufer ★ 2.5k
Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created? For myself, if …
Comment: Align miRNA library (small RNA-seq) without trimming by Paola ▴ 10
Hi Ming Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming by Ming Tommy Tang ★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression by afei • 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa by rebeliscu ▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an by cfos4698 ▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking by Mensur Dlakic ★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error by Declan • 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43 by ahmad • 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43 by ahmad • 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq by dsull ★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq by dsull ★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell by lethalfang ▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set by lethalfang ▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata? by jv ★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
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