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113,890 results • Page
3 of 2278
Sort: replies
Rank
Views
Votes
Replies
185
votes
43
replies
81k
views
29 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 24 days ago by
Ram
41k • written 13.7 years ago by
Yuri
★ 1.6k
11
votes
42
replies
3.7k
views
over presented kmer in fastq
fastqc
RNA-Seq
6.1 years ago by
Sam
▴ 150
8
votes
42
replies
4.3k
views
NaS (Nanopore Synthetic-long) help
Assembly
preprocessing
updated 11 months ago by
Ram
41k • written 8.5 years ago by
midox
▴ 290
151
votes
42
replies
178k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 18 months ago by
Ram
41k • written 11.7 years ago by
Obi Griffith
20k
57
votes
42
replies
6.0k
views
12 follow
Forum:
Why is academic software hard to install?
software-installation
updated 22 months ago by
Ram
41k • written 9.1 years ago by
lh3
33k
28
votes
42
replies
6.5k
views
7 follow
How to add tophat and bowtie to the path?
export PATH
bowtie2.2.9
tophat2
7.0 years ago by
mirza
▴ 180
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 8 months ago by
LauferVA
3.8k • written 10.5 years ago by
Whetting
★ 1.6k
23
votes
41
replies
3.6k
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 6 months ago by
Ram
41k • written 7 months ago by
Vijith
▴ 30
5
votes
41
replies
2.4k
views
Insert sequence in nt database
nt
3.5 years ago by
anasofiamoreira94
▴ 80
16
votes
41
replies
8.8k
views
How to extract information from headers of fasta file
sequence
updated 17 months ago by
Ram
41k • written 8.7 years ago by
Crystal
▴ 70
38
votes
41
replies
55k
views
9 follow
Volcano Plot from DEseq2
R
written 6.1 years ago by
1769mkc
★ 1.1k
170
votes
41
replies
93k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 10 weeks ago by
Ram
41k • written 12.5 years ago by
Palu
▴ 250
19
votes
41
replies
8.3k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.3 years ago by
ivivek_ngs
★ 5.2k • written 6.3 years ago by
sophialovechan
▴ 80
31
votes
41
replies
2.3k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 5 months ago by
Ram
41k • written 3.8 years ago by
K.Gee
▴ 40
16
votes
41
replies
2.1k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide
protein
6 weeks ago by
sil_bioinfo
▴ 30
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 9 months ago by
Ram
41k • written 9.0 years ago by
William
★ 5.2k
18
votes
41
replies
12k
views
6 follow
paired end illumina reads
Assembly
paired end
updated 16 months ago by
Ram
41k • written 8.1 years ago by
midox
▴ 290
26
votes
41
replies
15k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 12 months ago by
lovelymaoqin
• 0 • written 5.9 years ago by
BrunoGiotti
▴ 120
13
votes
41
replies
2.1k
views
Is my file created completely
sam
BWA-MEM
BWA
updated 8 months ago by
Ram
41k • written 6.6 years ago by
micro32uvas
▴ 10
98
votes
41
replies
5.4k
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 7 months ago by
Ram
41k • written 7.3 years ago by
moxu
▴ 510
18
votes
40
replies
17k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.4 years ago by
krishdb38
• 0 • written 7.4 years ago by
Esaie
▴ 170
10
votes
40
replies
6.0k
views
weird insert size post trimming
RNA-Seq
updated 6.3 years ago by
Gabriel R.
★ 2.9k • written 6.3 years ago by
badribio
▴ 280
67
votes
40
replies
9.0k
views
12 follow
Forum:
I want to re-open the old debate: python or perl ?
perl
python
updated 21 months ago by
Ram
41k • written 9.0 years ago by
Gabriel R.
★ 2.9k
6
votes
40
replies
10k
views
Fastx_Collapser Has No Fastq Output
fastx
RNA-seq
updated 9 months ago by
Ram
41k • written 10.2 years ago by
nbvasani
▴ 240
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 5.8 years ago by
Kevin Blighe
86k • written 7.1 years ago by
datascientist28
▴ 550
68
votes
40
replies
5.7k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen
sequencing
sequencing
updated 12.1 years ago by
pmenzel
▴ 310 • written 12.1 years ago by
Samuel Lampa
★ 1.3k
16
votes
40
replies
5.7k
views
About TCGA CNV data preprocessing
SNP
CNV
updated 5.1 years ago by
Kevin Blighe
86k • written 5.1 years ago by
Eric Wang
▴ 40
151
votes
39
replies
24k
views
20 follow
Forum:
A Farewell To Bioinformatics
bioinformatics
updated 9 months ago by
Ram
41k • written 10.9 years ago by
Martin A Hansen
3.0k
20
votes
39
replies
9.0k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast
blast
memory
updated 8.2 years ago by
Kumar
▴ 170 • written 11.9 years ago by
Amr
▴ 160
282
votes
39
replies
177k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 8 months ago by
Ram
41k • written 9.3 years ago by
Obi Griffith
20k
36
votes
39
replies
3.4k
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 6 months ago by
Ram
41k • written 6.1 years ago by
dhbradshaw
▴ 130
25
votes
39
replies
5.3k
views
8 follow
Forum:
Bioinformatics Study Group
study-group
updated 9 months ago by
Ram
41k • written 10.4 years ago by
Olivier
▴ 440
66
votes
39
replies
7.0k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career
subjective
updated 2.7 years ago by
Ram
41k • written 13.7 years ago by
Marcos De Carvalho
▴ 310
55
votes
39
replies
5.3k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf
python
perl
awk
updated 11.2 years ago by
Rm
8.2k • written 11.2 years ago by
Mahdi Sarmady
▴ 310
69
votes
39
replies
4.1k
views
14 follow
Forum:
Preparation for Bioinformatics.SE closing
meta
biostars
updated 6 months ago by
Ram
41k • written 6.5 years ago by
John
13k
11
votes
39
replies
3.7k
views
Any advice for a de novo genome assembly
k-mer
de novo
genome
assembly
updated 7.0 years ago by
krsahlin
▴ 60 • written 7.0 years ago by
Picasa
▴ 640
18
votes
39
replies
3.7k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 6 months ago by
Ram
41k • written 4.6 years ago by
chernouhov sergey
▴ 50
81
votes
39
replies
7.0k
views
11 follow
News:
State Of Biostar - Future Directions (January 2013)
biostars
updated 9 months ago by
Ram
41k • written 10.9 years ago by
Istvan Albert
99k
226
votes
39
replies
286k
views
33 follow
Gene Id Conversion Tool
david
updated 6 weeks ago by
Ram
41k • written 14.1 years ago by
Renee
▴ 620
95
votes
39
replies
147k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 7 months ago by
Dan
▴ 160 • written 11.4 years ago by
abi
▴ 380
39
votes
38
replies
8.0k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 15 months ago by
Ram
41k • written 8.1 years ago by
John
13k
100
votes
38
replies
29k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 9 days ago by
Jeremy Leipzig
22k • written 10.1 years ago by
14134125465346445
★ 3.6k
231
votes
38
replies
142k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 5 months ago by
Ram
41k • written 10.8 years ago by
Malachi Griffith
19k
48
votes
38
replies
16k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
software
genome
annotation
updated 8 months ago by
Ram
41k • written 7.7 years ago by
Eric Normandeau
11k
27
votes
38
replies
19k
views
Heatmap based with FPKM values
RNA-Seq
next-gen
R
updated 4.6 years ago by
Biostar
20 • written 6.0 years ago by
Mehmet
▴ 820
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 19 months ago by
Ram
41k • written 8.8 years ago by
Mo
▴ 920
53
votes
38
replies
4.1k
views
10 follow
Multiple alignment software
alignment
clustal omega
tcoffee
updated 4.2 years ago by
Istvan Albert
99k • written 4.2 years ago by
juanjo75es
▴ 130
129
votes
38
replies
7.2k
views
21 follow
Forum:
Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 6 months ago by
Ram
41k • written 4.7 years ago by
Istvan Albert
99k
47
votes
37
replies
8.2k
views
12 follow
Forum:
The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 9 months ago by
Ram
41k • written 10.3 years ago by
Niallhaslam
2.3k
29
votes
37
replies
3.1k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf
ped
phased
5.1 years ago by
Shicheng Guo
★ 9.3k
113,890 results • Page
3 of 2278
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
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Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
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GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts
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Gama313
▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
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by
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My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
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99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
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You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
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CTLong
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Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
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ayasu
• 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts
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Brian Bushnell
19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
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Brian Bushnell
19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in
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★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
Brian Bushnell
19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters?
by
AMARU
• 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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