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112,644 results • Page 3 of 2253
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11
votes
42
replies
3.4k
views
over presented kmer in fastq
fastqc RNA-Seq
6.0 years ago by Sam ▴ 150
8
votes
42
replies
4.1k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 8 months ago by 40k • written 8.3 years ago by ▴ 290
122
votes
42
replies
9.4k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 7 months ago by 40k • written 10.8 years ago by 98k
138
votes
42
replies
21k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 6 months ago by 3.7k • written 10.3 years ago by ★ 1.6k
57
votes
42
replies
5.8k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 20 months ago by 40k • written 8.9 years ago by 33k
28
votes
42
replies
6.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
6.8 years ago by mirza ▴ 180
203
votes
41
replies
24k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 7 months ago by 40k • written 8.9 years ago by ★ 5.2k
13
votes
41
replies
1.9k
views
Is my file created completely
sam BWA-MEM BWA
updated 6 months ago by 40k • written 6.4 years ago by ▴ 10
5
votes
41
replies
2.3k
views
Insert sequence in nt database
nt
3.4 years ago by anasofiamoreira94 ▴ 80
19
votes
41
replies
8.0k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by ▴ 80
31
votes
41
replies
2.0k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 3 months ago by 40k • written 3.6 years ago by ▴ 40
18
votes
41
replies
12k
views
6 follow
paired end illumina reads
Assembly paired end
updated 14 months ago by 40k • written 7.9 years ago by ▴ 290
23
votes
41
replies
3.1k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS biopython illumina WGS
updated 4 months ago by 40k • written 5 months ago by ▴ 30
98
votes
41
replies
5.1k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error next-gen-sequencing
updated 5 months ago by 40k • written 7.1 years ago by ▴ 510
16
votes
41
replies
8.4k
views
How to extract information from headers of fasta file
sequence
updated 15 months ago by 40k • written 8.5 years ago by ▴ 70
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 3 days ago by 40k • written 12.3 years ago by ▴ 250
38
votes
41
replies
54k
views
9 follow
Volcano Plot from DEseq2
R
written 5.9 years ago by ★ 1.1k
26
votes
41
replies
15k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 10 months ago by • 0 • written 5.7 years ago by ▴ 120
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.2 years ago by ▴ 170
6
votes
40
replies
9.8k
views
Fastx_Collapser Has No Fastq Output
fastx RNA-seq
updated 6 months ago by 40k • written 10.0 years ago by ▴ 240
68
votes
40
replies
5.4k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen sequencing sequencing
updated 11.9 years ago by ▴ 310 • written 11.9 years ago by ★ 1.3k
10
votes
40
replies
5.6k
views
weird insert size post trimming
RNA-Seq
updated 6.1 years ago by ★ 2.9k • written 6.1 years ago by ▴ 280
40
votes
40
replies
10k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq alignment
updated 5.6 years ago by 86k • written 7.0 years ago by ▴ 550
16
votes
40
replies
5.4k
views
About TCGA CNV data preprocessing
SNP CNV
updated 5.0 years ago by 86k • written 5.0 years ago by ▴ 40
67
votes
40
replies
8.7k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 19 months ago by 40k • written 8.9 years ago by ★ 2.9k
151
votes
39
replies
23k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 7 months ago by 40k • written 10.7 years ago by 3.0k
20
votes
39
replies
8.6k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast blast memory
updated 8.0 years ago by ▴ 170 • written 11.7 years ago by ▴ 160
226
votes
39
replies
284k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 13 months ago by 40k • written 13.9 years ago by ▴ 620
69
votes
39
replies
3.8k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 4 months ago by 40k • written 6.3 years ago by 13k
25
votes
39
replies
5.0k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 7 months ago by 40k • written 10.2 years ago by ▴ 440
66
votes
39
replies
6.9k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career subjective
updated 2.5 years ago by 40k • written 13.5 years ago by ▴ 310
55
votes
39
replies
5.0k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf python perl awk
updated 11.1 years ago by 8.2k • written 11.1 years ago by ▴ 310
18
votes
39
replies
3.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 4 months ago by 40k • written 4.5 years ago by ▴ 50
11
votes
39
replies
3.4k
views
Any advice for a de novo genome assembly
k-mer de novo genome assembly
updated 6.8 years ago by ▴ 60 • written 6.9 years ago by ▴ 640
81
votes
39
replies
6.6k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 7 months ago by 40k • written 10.7 years ago by 98k
93
votes
39
replies
142k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by ▴ 140 • written 11.2 years ago by ▴ 380
36
votes
39
replies
3.2k
views
11 follow
Forum: Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast RNA-Seq alignment next-gen-sequencing
updated 4 months ago by 40k • written 5.9 years ago by ▴ 130
282
votes
39
replies
174k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 26 days ago by 21k • written 9.9 years ago by ★ 3.6k
129
votes
38
replies
6.7k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 3 months ago by 40k • written 4.5 years ago by 98k
229
votes
38
replies
140k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 3 months ago by 40k • written 10.6 years ago by 19k
53
votes
38
replies
3.8k
views
10 follow
Multiple alignment software
alignment clustal omega tcoffee
updated 4.0 years ago by 98k • written 4.0 years ago by ▴ 130
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 17 months ago by 40k • written 8.6 years ago by ▴ 920
48
votes
38
replies
16k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 5 months ago by 40k • written 7.5 years ago by 11k
39
votes
38
replies
7.7k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 13 months ago by 40k • written 7.9 years ago by 13k
27
votes
38
replies
19k
views
Heatmap based with FPKM values
RNA-Seq next-gen R
updated 4.4 years ago by 20 • written 5.9 years ago by ▴ 820
47
votes
37
replies
7.9k
views
12 follow
Forum: The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 7 months ago by 40k • written 10.1 years ago by 2.3k
29
votes
37
replies
2.9k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf ped phased
4.9 years ago by Shicheng Guo ★ 9.3k
43
votes
37
replies
1.9k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 4 months ago by 40k • written 6.0 years ago by ★ 4.2k
87
votes
37
replies
49k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 18 months ago by 40k • written 10.2 years ago by ▴ 110
112,644 results • Page 3 of 2253
Recent Votes
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
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Recent Replies
Comment: Violin plot (Monocle 3) - Troubleshooting by fracarb8 ★ 1.2k
You did not add the screenshot.
Answer: BED files by Alex Reynolds 35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by dariober 14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files by barslmn ★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors by Alex Reynolds 35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file by Alex Reynolds 35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file by barslmn ★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ? by barslmn ★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase by Barry Digby ★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups by ATpoint 76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups by edus_bioinfo ▴ 40
To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise by ATpoint 76k
You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups by Basti ★ 1.7k
Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file by Patrick • 0
Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
Answer: Average Coverage after Assembly (Spades) by taniapsduarte • 0
Hi, I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!
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