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103
votes
34
replies
113k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 3 months ago by 43k • written 11.9 years ago by ▴ 390
16
votes
34
replies
4.8k
views
7 follow
GC percent detection for several number of genes
GC% large number of genes
7.1 years ago by nazaninhoseinkhan ▴ 520
12
votes
34
replies
5.1k
views
Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fixing Explanations
sequencing
updated 12.1 years ago by ★ 1.3k • written 12.6 years ago by ▴ 200
41
votes
34
replies
16k
views
10 follow
Best tool for variant calling
SNP genome alignment next-gen
updated 5.4 years ago by • 0 • written 5.9 years ago by ▴ 510
19
votes
34
replies
5.7k
views
6 follow
How can I convert the blast results into a matrix?
perl linux python blast
updated 2.2 years ago by 43k • written 9.4 years ago by ▴ 150
16
votes
34
replies
12k
views
6 follow
Why am I unable to load my data from a tab separated file into R?
microarray programming R
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 920
54
votes
34
replies
4.9k
views
13 follow
Forum: Should We Release Database Dumps Of All Questions On Biostar?
meta biostars
updated 14 months ago by 43k • written 13.4 years ago by 100k
31
votes
34
replies
7.4k
views
11 follow
Forum: pros- and cons- : programming skills vs. GUI
programming lecture
updated 12 months ago by 43k • written 8.4 years ago by ★ 4.7k
147
votes
34
replies
55k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 14 months ago by 43k • written 11.0 years ago by 6.0k
15
votes
34
replies
12k
views
Improving efficiency of awk for large files
awk
updated 18 months ago by 43k • written 8.7 years ago by ▴ 350
44
votes
34
replies
13k
views
7 follow
Technical replicates in RNAseq
RNA-Seq technical_replicates
2.1 years ago by grant.hovhannisyan ★ 2.6k
2
votes
34
replies
6.8k
views
How to install pip on HPC server
software error
6.2 years ago by Bioinfonext ▴ 460
80
votes
34
replies
5.2k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 15 months ago by 43k • written 8.9 years ago by ▴ 520
65
votes
34
replies
27k
views
20 follow
Phylogenetic Analysis Of Whole Genomes
phylogenetics tree
updated 2.1 years ago by 43k • written 13.7 years ago by ▴ 130
11
votes
34
replies
2.2k
views
De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
RNA-Seq read support Assembly bowtie2
3.6 years ago by Dunois ★ 2.5k
172
votes
34
replies
26k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r books bioconductor
updated 5 months ago by 43k • written 14.1 years ago by 54k
12
votes
33
replies
3.1k
views
Missing sequences in local NT database
nt blast ncbi blastdbcmd
updated 5.5 years ago by 15k • written 5.5 years ago by ★ 2.7k
138
votes
33
replies
66k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 18 months ago by 43k • written 10.0 years ago by ▴ 490
143
votes
33
replies
30k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 5.0 years ago by ▴ 50 • written 13.8 years ago by 13k
70
votes
33
replies
17k
views
18 follow
Choosing Random Set Of Seqs From Larger Set
random fasta
updated 24 months ago by 43k • written 12.1 years ago by ▴ 190
16
votes
33
replies
8.4k
views
9 follow
Back-filling missing genotypes in merged VCF
vcf
updated 16 months ago by 161k • written 9.5 years ago by ★ 1.1k
48
votes
33
replies
43k
views
16 follow
Extract A Group Of Fasta Sequences From A File
fasta python perl biopython bioperl
updated 2.4 years ago by 43k • written 13.8 years ago by ▴ 60
6
votes
33
replies
2.8k
views
I need to understand this image
phylogenies
updated 7.2 years ago by 23k • written 7.2 years ago by • 0
24
votes
33
replies
8.5k
views
Contribute To The Nat Gen Paper "Principles For The Post-Gwas Functional Characterisation Of Risk Loci"
gwas snp
updated 13.4 years ago by 18k • written 13.4 years ago by 28k
121
votes
33
replies
39k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by ★ 2.5k • written 10.7 years ago by 11k
27
votes
33
replies
3.8k
views
7 follow
Forum: Biostars question catagories
statistics biostars meta
updated 12 months ago by 43k • written 7.5 years ago by 13k
298
votes
33
replies
108k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 14 months ago by 43k • written 10.5 years ago by 20k
27
votes
33
replies
17k
views
high % of reads mapped to multiple loci after STAR mapping
RNA-Seq STAR single-end
updated 6.4 years ago by ▴ 990 • written 6.4 years ago by ★ 1.2k
10
votes
33
replies
3.8k
views
Looking for a tool like fastq screen but for ONT data
gridion nanopore ont minion
updated 10 months ago by 43k • written 5.8 years ago by ★ 1.4k
41
votes
33
replies
18k
views
10 follow
How To Convert Xml Into A Decent Parseable Format?
xml parsing perl subjective
updated 12.9 years ago by ▴ 30 • written 12.9 years ago by ★ 2.3k
29
votes
33
replies
8.1k
views
12 follow
getBM error while using bioMart
biomart getBM ensembl
updated 3.5 years ago by • 0 • written 3.5 years ago by ▴ 160
11
votes
33
replies
4.0k
views
Detect Regions In A List That Are Within 1 Megabase Of Each Other
python snp genomics overlap
updated 12.5 years ago by 54k • written 12.5 years ago by ▴ 350
11
votes
33
replies
17k
views
How we can analyze sanger sequence chromatogram?
SNP sequencing alignment sanger
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 40
50
votes
33
replies
55k
views
10 follow
I would like to add gene names to a volcano plot obtained from DEseq2
RNA-Seq DEseq2 R
updated 6.0 years ago by 87k • written 7.7 years ago by ▴ 340
0
votes
32
replies
9.4k
views
DoHeatmap clusters, Seurat pipeline
scRNA-sequencing
3.6 years ago by Morris_Chair ▴ 350
10
votes
32
replies
3.7k
views
6 follow
Why my CD31+ endothelial cells RNAseq didn't express CD31?
CD31 HISAT2 endothelialcells Stringtie RNAseq
3.0 years ago by Youyy • 0
93
votes
32
replies
33k
views
26 follow
Linux Distros Best Suited For Bioinformatics?
linux
written 12.2 years ago by ▴ 150
32
votes
32
replies
8.0k
views
11 follow
Should We Be Using Much More Json In Our Delimited Data Formats?
gff vcf
updated 13.2 years ago by ★ 2.4k • written 13.2 years ago by ★ 3.3k
88
votes
32
replies
9.5k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 2.1 years ago by 43k • written 9.5 years ago by 161k
82
votes
32
replies
7.7k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 14 months ago by 43k • written 11.4 years ago by ★ 3.6k
153
votes
32
replies
8.5k
views
23 follow
Picking A Programming Language And Where To Begin
programming next-gen sequencing c subjective
updated 12.2 years ago by ▴ 60 • written 12.7 years ago by ★ 2.8k
53
votes
32
replies
13k
views
13 follow
Bio-Javascript?
updated 2.0 years ago by 43k • written 13.2 years ago by ★ 3.1k
3
votes
32
replies
3.4k
views
fastqc report for degradome reads
fastqc adaptor
6.0 years ago by Sam ▴ 150
9
votes
32
replies
3.0k
views
Differentially gene expressed analyses of two different samples
RNA-Seq R next-gen rna-seq
updated 7.4 years ago by ▴ 610 • written 7.4 years ago by ▴ 820
129
votes
32
replies
129k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 2.1 years ago by 43k • written 13.1 years ago by ▴ 540
9
votes
31
replies
4.9k
views
6 follow
Clustering Million Points : Transcript Start And End Sites
clustering
updated 12.0 years ago by 18k • written 12.1 years ago by ★ 1.6k
59
votes
31
replies
4.9k
views
12 follow
News: Example of how bioinformaticians can publish in Scientific Reports (by nature publishing group) using publicly available NGS data
publication NGS
updated 12 months ago by 43k • written 7.3 years ago by 11k
147
votes
31
replies
137k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 9 months ago by 43k • written 12.2 years ago by ★ 2.9k
38
votes
31
replies
2.8k
views
10 follow
Forum: To the Biologists out there: What bioinf tool are you missing?
education career
updated 12 months ago by 43k • written 7.7 years ago by ▴ 180
17
votes
31
replies
5.7k
views
Finding the best model for expression data (RNA-Seq counts)
RNA-Seq glm model fit regression
updated 5.1 years ago by 19k • written 5.1 years ago by ▴ 250
1,000 results • Page 5 of 20
Recent Votes
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
Comment: Bwa sampe - BGI
Comment: Redirection of Duplicate PMIDs
Answer: Redirection of Duplicate PMIDs
A: Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To
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Recent Replies
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus by GenoMax 141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database by Art1ess • 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection by LauferVA 4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024 by geneontologyhelp ▴ 360
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Let us know when you find out. Would be a useful thing to know what the data looks like.
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Yes, that is a very good idea. Thanks for the help!
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Only thing would be to try them out. See if you can detect them in the data you have. You could also simply look for unique representativ…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by GenoMax 141k
`clustal omega` can calculate distance matrix between two proteins (makes sense if your proteins are of similar size). You could try that: …
Comment: Should I use unpaired reads from trimmomatic by swbarnes2 14k
If the unpaired are _2, files, the _1 must exist somewhere. But the simple answer is probably going to be to just use all the _2 only. Yo…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by GenoMax 141k
> The needless granularity (fake precision) was obvious from the start You are assuming that all data generated is always of great quality…
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