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117,001 results • Page 3 of 2341
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66
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43
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27k
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23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen sequencing parsing fastq programming
updated 2.3 years ago by 43k • written 13.3 years ago by ★ 2.2k
57
votes
43
replies
16k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
NGS alignment genome RNA-Seq sequence
updated 14 months ago by 43k • written 5.3 years ago by 11k
8
votes
42
replies
4.7k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 16 months ago by 43k • written 9.0 years ago by ▴ 290
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 5 weeks ago by 22k • written 10.5 years ago by ★ 3.6k
11
votes
42
replies
4.2k
views
over presented kmer in fastq
fastqc RNA-Seq
6.6 years ago by Sam ▴ 150
138
votes
42
replies
22k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 13 months ago by 4.2k • written 10.9 years ago by ★ 1.6k
57
votes
42
replies
6.7k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 2.3 years ago by 43k • written 9.6 years ago by 33k
151
votes
42
replies
180k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 24 months ago by 43k • written 12.2 years ago by 20k
28
votes
42
replies
7.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
7.4 years ago by mirza ▴ 180
23
votes
41
replies
4.5k
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 12 months ago by 43k • written 13 months ago by ▴ 30
31
votes
41
replies
2.8k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 11 months ago by 43k • written 4.2 years ago by ▴ 40
98
votes
41
replies
6.2k
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 13 months ago by 43k • written 7.7 years ago by ▴ 510
26
votes
41
replies
17k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 18 months ago by • 0 • written 6.3 years ago by ▴ 120
16
votes
41
replies
9.6k
views
How to extract information from headers of fasta file
sequence
updated 23 months ago by 43k • written 9.2 years ago by ▴ 70
18
votes
41
replies
14k
views
6 follow
paired end illumina reads
Assembly paired end
updated 22 months ago by 43k • written 8.6 years ago by ▴ 290
18
votes
41
replies
3.6k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide protein
updated 5 months ago by 21k • written 7 months ago by ▴ 40
38
votes
41
replies
60k
views
9 follow
Volcano Plot from DEseq2
R
written 6.5 years ago by ★ 1.2k
5
votes
41
replies
3.0k
views
Insert sequence in nt database
nt
4.0 years ago by anasofiamoreira94 ▴ 80
203
votes
41
replies
25k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 15 months ago by 43k • written 9.5 years ago by ★ 5.3k
19
votes
41
replies
9.3k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by ▴ 80
171
votes
41
replies
98k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 7 months ago by 43k • written 12.9 years ago by ▴ 250
13
votes
41
replies
2.4k
views
Is my file created completely
sam BWA-MEM BWA
updated 14 months ago by 43k • written 7.0 years ago by ▴ 10
18
votes
40
replies
18k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.9 years ago by • 0 • written 7.9 years ago by ▴ 170
40
votes
40
replies
11k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq alignment
updated 6.2 years ago by 88k • written 7.6 years ago by ▴ 560
16
votes
40
replies
6.4k
views
About TCGA CNV data preprocessing
SNP CNV
updated 5.6 years ago by 88k • written 5.6 years ago by ▴ 50
68
votes
40
replies
6.5k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen sequencing sequencing
updated 12.6 years ago by ▴ 310 • written 12.6 years ago by ★ 1.3k
6
votes
40
replies
11k
views
Fastx_Collapser Has No Fastq Output
fastx RNA-seq
updated 14 months ago by 43k • written 10.7 years ago by ▴ 240
67
votes
40
replies
9.7k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 2.2 years ago by 43k • written 9.5 years ago by ★ 2.9k
10
votes
40
replies
6.6k
views
weird insert size post trimming
RNA-Seq
updated 6.7 years ago by ★ 2.9k • written 6.8 years ago by ▴ 290
151
votes
39
replies
25k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 14 months ago by 43k • written 11.3 years ago by 3.0k
20
votes
39
replies
9.9k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast blast memory
updated 8.7 years ago by ▴ 170 • written 12.3 years ago by ▴ 160
11
votes
39
replies
4.2k
views
Any advice for a de novo genome assembly
k-mer de novo genome assembly
updated 7.5 years ago by ▴ 60 • written 7.5 years ago by ▴ 640
69
votes
39
replies
4.7k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 12 months ago by 43k • written 7.0 years ago by 13k
25
votes
39
replies
5.9k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 14 months ago by 43k • written 10.9 years ago by ▴ 440
98
votes
39
replies
159k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 13 months ago by ▴ 180 • written 11.9 years ago by ▴ 390
55
votes
39
replies
5.8k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf python perl awk
updated 11.7 years ago by 8.3k • written 11.7 years ago by ▴ 310
36
votes
39
replies
4.2k
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 12 months ago by 43k • written 6.5 years ago by ▴ 130
66
votes
39
replies
7.5k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career subjective
updated 3.1 years ago by 43k • written 14.2 years ago by ▴ 310
288
votes
39
replies
184k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 14 months ago by 43k • written 9.7 years ago by 20k
226
votes
39
replies
289k
views
33 follow
Gene Id Conversion Tool
david
updated 7 months ago by 43k • written 14.6 years ago by ▴ 620
18
votes
39
replies
4.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 12 months ago by 43k • written 5.1 years ago by ▴ 50
81
votes
39
replies
7.6k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 15 months ago by 43k • written 11.4 years ago by 100k
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 11 weeks ago by ▴ 60 • written 7.9 years ago by 6.6k
27
votes
38
replies
20k
views
Heatmap based with FPKM values
RNA-Seq next-gen R
updated 5.0 years ago by 20 • written 6.5 years ago by ▴ 820
231
votes
38
replies
146k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 11 months ago by 43k • written 11.2 years ago by 20k
129
votes
38
replies
8.3k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 11 months ago by 43k • written 5.1 years ago by 100k
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 920
53
votes
38
replies
4.6k
views
10 follow
Multiple alignment software
alignment clustal omega tcoffee
updated 4.7 years ago by 100k • written 4.7 years ago by ▴ 130
48
votes
38
replies
17k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 13 months ago by 43k • written 8.2 years ago by 11k
39
votes
38
replies
9.1k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 21 months ago by 43k • written 8.5 years ago by 13k
117,001 results • Page 3 of 2341
Recent Votes
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
How can I perform Differential expression analysis with just one control and one cancer sample?
Comment: scRNAseq Differential expression analysis
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Recent Replies
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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