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1,000 results • Page 3 of 20
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16
votes
43
replies
6.7k
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Stuck on calculating principal components
Vegan R software error SNP
updated 6.4 years ago by ▴ 280 • written 6.4 years ago by ★ 4.3k
66
votes
43
replies
27k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen sequencing parsing fastq programming
updated 2.2 years ago by 43k • written 13.3 years ago by ★ 2.2k
57
votes
42
replies
6.6k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 2.2 years ago by 43k • written 9.5 years ago by 33k
8
votes
42
replies
4.7k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 15 months ago by 43k • written 8.9 years ago by ▴ 290
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 23 months ago by 43k • written 12.1 years ago by 20k
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
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 16 days ago by 22k • written 10.4 years ago by ★ 3.6k
28
votes
42
replies
7.1k
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
11
votes
42
replies
4.1k
views
over presented kmer in fastq
fastqc RNA-Seq
6.5 years ago by Sam ▴ 150
23
votes
41
replies
4.3k
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 11 months ago by 43k • written 12 months ago by ▴ 30
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
98
votes
41
replies
6.1k
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 12 months ago by 43k • written 7.6 years ago by ▴ 510
31
votes
41
replies
2.7k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 10 months ago by 43k • written 4.2 years ago by ▴ 40
18
votes
41
replies
3.4k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide protein
updated 4 months ago by 21k • written 6 months ago by ▴ 40
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 14 months ago by 43k • written 9.4 years ago by ★ 5.3k
5
votes
41
replies
2.9k
views
Insert sequence in nt database
nt
3.9 years ago by anasofiamoreira94 ▴ 80
13
votes
41
replies
2.4k
views
Is my file created completely
sam BWA-MEM BWA
updated 13 months ago by 43k • written 7.0 years ago by ▴ 10
19
votes
41
replies
9.1k
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
26
votes
41
replies
17k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 17 months ago by • 0 • written 6.3 years ago by ▴ 120
18
votes
41
replies
14k
views
6 follow
paired end illumina reads
Assembly paired end
updated 21 months ago by 43k • written 8.5 years ago by ▴ 290
16
votes
41
replies
9.5k
views
How to extract information from headers of fasta file
sequence
updated 22 months ago by 43k • written 9.1 years ago by ▴ 70
38
votes
41
replies
59k
views
9 follow
Volcano Plot from DEseq2
R
written 6.5 years ago by ★ 1.2k
18
votes
40
replies
18k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.8 years ago by • 0 • written 7.8 years ago by ▴ 170
6
votes
40
replies
11k
views
Fastx_Collapser Has No Fastq Output
fastx RNA-seq
updated 14 months ago by 43k • written 10.6 years ago by ▴ 240
10
votes
40
replies
6.5k
views
weird insert size post trimming
RNA-Seq
updated 6.7 years ago by ★ 2.9k • written 6.7 years ago by ▴ 290
16
votes
40
replies
6.2k
views
About TCGA CNV data preprocessing
SNP CNV
updated 5.5 years ago by 87k • written 5.5 years ago by ▴ 50
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 87k • written 7.5 years ago by ▴ 560
68
votes
40
replies
6.4k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen sequencing sequencing
updated 12.5 years ago by ▴ 310 • written 12.5 years ago by ★ 1.3k
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 9.4 years ago by ★ 2.9k
151
votes
39
replies
25k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 14 months ago by 43k • written 11.2 years ago by 3.0k
20
votes
39
replies
9.8k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast blast memory
updated 8.6 years ago by ▴ 170 • written 12.3 years ago by ▴ 160
81
votes
39
replies
7.5k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 14 months ago by 43k • written 11.3 years ago by 100k
36
votes
39
replies
4.1k
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 11 months ago by 43k • written 6.5 years ago by ▴ 130
11
votes
39
replies
4.2k
views
Any advice for a de novo genome assembly
k-mer de novo genome assembly
updated 7.4 years ago by ▴ 60 • written 7.4 years ago by ▴ 640
18
votes
39
replies
4.2k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 11 months ago by 43k • written 5.0 years ago by ▴ 50
98
votes
39
replies
157k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 12 months ago by ▴ 180 • written 11.8 years ago by ▴ 390
25
votes
39
replies
5.8k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 14 months ago by 43k • written 10.8 years ago by ▴ 440
287
votes
39
replies
183k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 13 months ago by 43k • written 9.7 years ago by 20k
69
votes
39
replies
4.6k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 11 months ago by 43k • written 6.9 years ago by 13k
66
votes
39
replies
7.4k
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 14.1 years ago by ▴ 310
55
votes
39
replies
5.7k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf python perl awk
updated 11.6 years ago by 8.3k • written 11.6 years ago by ▴ 310
226
votes
39
replies
288k
views
33 follow
Gene Id Conversion Tool
david
updated 6 months ago by 43k • written 14.5 years ago by ▴ 620
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 7 weeks ago by ▴ 60 • written 7.8 years ago by 6.5k
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 920
39
votes
38
replies
8.9k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 20 months ago by 43k • written 8.5 years ago by 13k
48
votes
38
replies
17k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 12 months ago by 43k • written 8.1 years ago by 11k
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 10 months ago by 43k • written 11.2 years ago by 19k
53
votes
38
replies
4.5k
views
10 follow
Multiple alignment software
alignment clustal omega tcoffee
updated 4.6 years ago by 100k • written 4.6 years ago by ▴ 130
129
votes
38
replies
8.2k
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
27
votes
38
replies
20k
views
Heatmap based with FPKM values
RNA-Seq next-gen R
updated 5.0 years ago by 20 • written 6.4 years ago by ▴ 820
1,000 results • Page 3 of 20
Recent Votes
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Recent Replies
Comment: Why cd-hit-est not work when sequence identity threshold<0.95？ by Dateline • 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq by Kevin Blighe 87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies by Kevin Blighe 87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue by emmanouil.a ▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package by Pierre Lindenbaum 161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation by Lissa Cruz Saavedra • 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file by swbarnes2 14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model by biochugs • 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed) by Jeremy ▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination by DKA ▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed) by Mensur Dlakic ★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model by Mensur Dlakic ★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed) by Jeremy ▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file by GenoMax 141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
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