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155
votes
44
replies
32k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 22 months ago by 43k • written 10.3 years ago by ★ 2.1k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram visualization chromosome
updated 8 weeks ago by 54k • written 14.2 years ago by ★ 1.7k
102
votes
44
replies
9.1k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 14 months ago by 43k • written 10.8 years ago by 24k
1
vote
43
replies
4.1k
views
Database from .gbk files
database gbk ncbi
updated 13 months ago by • 0 • written 3.9 years ago by ▴ 10
31
votes
43
replies
20k
views
11 follow
Volcano plot help code
R rna-seq
updated 5.9 years ago by ▴ 480 • written 6.1 years ago by ▴ 80
19
votes
43
replies
5.7k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by nazaninhoseinkhan ▴ 520
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 2.3 years ago by 43k • written 13.3 years ago by ★ 2.2k
16
votes
43
replies
6.8k
views
Stuck on calculating principal components
Vegan R software error SNP
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ★ 4.3k
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
11
votes
42
replies
4.2k
views
over presented kmer in fastq
fastqc RNA-Seq
6.6 years ago by Sam ▴ 150
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
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
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
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
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
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
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
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
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
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
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
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
110
votes
37
replies
8.6k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 15 months ago by 43k • written 12.6 years ago by 161k
29
votes
37
replies
3.5k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf ped phased
5.5 years ago by Shicheng Guo ★ 9.4k
10
votes
37
replies
13k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 5 weeks ago by • 0 • written 8.9 years ago by ▴ 170
87
votes
37
replies
52k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 2.2 years ago by 43k • written 10.8 years ago by ▴ 110
36
votes
37
replies
17k
views
6 follow
How to cluster genes in heatmap
RNA-Seq R gene
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 820
17
votes
37
replies
4.8k
views
No alias or index file found for protein database
next-gen software error sequence
updated 5.0 years ago by 20 • written 5.1 years ago by ▴ 520
5
votes
37
replies
3.6k
views
search text in one file and then replace with text from another file
search replace multiple files
6.6 years ago by mforthman ▴ 50
130
votes
37
replies
14k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 12.7 years ago by ★ 1.3k • written 12.7 years ago by ▴ 820
18
votes
37
replies
13k
views
11 follow
Is it possible to download the full EpiCov database from GISAID?
GISAID genome Database EpiCoV
updated 3.1 years ago by ▴ 290 • written 4.2 years ago by ▴ 30
16
votes
37
replies
18k
views
7 follow
extracting the soft clipped seq only from a sam file
sam bam soft clip
updated 7.8 years ago by 20 • written 9.4 years ago by ★ 1.3k
40
votes
36
replies
14k
views
9 follow
Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score does not seem to do the trick in my case)
next-gen alignment bwa
updated 7.0 years ago by 13k • written 7.0 years ago by ▴ 130
3
votes
36
replies
5.2k
views
inquiry related to snpsift
rsid snp vcf
updated 2.8 years ago by 88k • written 2.8 years ago by ▴ 140
1,000 results • Page 2 of 20
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Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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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
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Recent Replies
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
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. Table 1 o…
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…
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