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116,743 results • Page
3 of 2335
Sort: replies
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Views
Votes
Replies
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
Ram
43k • written 13.3 years ago by
toni
★ 2.2k
19
votes
43
replies
5.6k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by
nazaninhoseinkhan
▴ 520
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 24 days ago by
Jeremy Leipzig
22k • written 10.5 years ago by
14134125465346445
★ 3.6k
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
Ram
43k • written 9.6 years ago by
lh3
33k
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
LauferVA
4.2k • written 10.9 years ago by
Whetting
★ 1.6k
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 23 months ago by
Ram
43k • written 12.2 years ago by
Obi Griffith
20k
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
8
votes
42
replies
4.7k
views
NaS (Nanopore Synthetic-long) help
Assembly
preprocessing
updated 16 months ago by
Ram
43k • written 8.9 years ago by
midox
▴ 290
23
votes
41
replies
4.4k
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
Ram
43k • written 12 months ago by
Vijith
▴ 30
16
votes
41
replies
9.6k
views
How to extract information from headers of fasta file
sequence
updated 22 months ago by
Ram
43k • written 9.1 years ago by
Crystal
▴ 70
19
votes
41
replies
9.2k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.7 years ago by
ivivek_ngs
★ 5.2k • written 6.7 years ago by
sophialovechan
▴ 80
18
votes
41
replies
14k
views
6 follow
paired end illumina reads
Assembly
paired end
updated 22 months ago by
Ram
43k • written 8.5 years ago by
midox
▴ 290
38
votes
41
replies
60k
views
9 follow
Volcano Plot from DEseq2
R
written 6.5 years ago by
1769mkc
★ 1.2k
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
Ram
43k • written 9.5 years ago by
William
★ 5.3k
5
votes
41
replies
2.9k
views
Insert sequence in nt database
nt
4.0 years ago by
anasofiamoreira94
▴ 80
26
votes
41
replies
17k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 17 months ago by
lovelymaoqin
• 0 • written 6.3 years ago by
BrunoGiotti
▴ 120
13
votes
41
replies
2.4k
views
Is my file created completely
sam
BWA-MEM
BWA
updated 13 months ago by
Ram
43k • written 7.0 years ago by
micro32uvas
▴ 10
18
votes
41
replies
3.5k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide
protein
updated 4 months ago by
Joe
21k • written 7 months ago by
sil_bioinfo
▴ 40
171
votes
41
replies
98k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 7 months ago by
Ram
43k • written 12.9 years ago by
Palu
▴ 250
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
Ram
43k • written 7.7 years ago by
moxu
▴ 510
31
votes
41
replies
2.7k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 11 months ago by
Ram
43k • written 4.2 years ago by
K.Gee
▴ 40
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
krishdb38
• 0 • written 7.9 years ago by
Esaie
▴ 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
Kevin Blighe
87k • written 7.6 years ago by
datascientist28
▴ 560
6
votes
40
replies
11k
views
Fastx_Collapser Has No Fastq Output
fastx
RNA-seq
updated 14 months ago by
Ram
43k • written 10.6 years ago by
nbvasani
▴ 240
10
votes
40
replies
6.6k
views
weird insert size post trimming
RNA-Seq
updated 6.7 years ago by
Gabriel R.
★ 2.9k • written 6.7 years ago by
badribio
▴ 290
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
Ram
43k • written 9.5 years ago by
Gabriel R.
★ 2.9k
16
votes
40
replies
6.3k
views
About TCGA CNV data preprocessing
SNP
CNV
updated 5.6 years ago by
Kevin Blighe
87k • written 5.6 years ago by
Eric Wang
▴ 50
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
pmenzel
▴ 310 • written 12.5 years ago by
Samuel Lampa
★ 1.3k
151
votes
39
replies
25k
views
20 follow
Forum:
A Farewell To Bioinformatics
bioinformatics
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Martin A Hansen
3.0k
20
votes
39
replies
9.9k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast
blast
memory
updated 8.6 years ago by
Kumar
▴ 170 • written 12.3 years ago by
Amr
▴ 160
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
krsahlin
▴ 60 • written 7.5 years ago by
Picasa
▴ 640
18
votes
39
replies
4.3k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 11 months ago by
Ram
43k • written 5.1 years ago by
chernouhov sergey
▴ 50
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
Ram
43k • written 6.5 years ago by
dhbradshaw
▴ 130
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
Rm
8.3k • written 11.7 years ago by
Mahdi Sarmady
▴ 310
69
votes
39
replies
4.6k
views
14 follow
Forum:
Preparation for Bioinformatics.SE closing
meta
biostars
updated 11 months ago by
Ram
43k • written 6.9 years ago by
John
13k
288
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
Ram
43k • written 9.7 years ago by
Obi Griffith
20k
98
votes
39
replies
158k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 12 months ago by
Dan
▴ 180 • written 11.8 years ago by
abi
▴ 390
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
Ram
43k • written 14.1 years ago by
Marcos De Carvalho
▴ 310
81
votes
39
replies
7.6k
views
11 follow
News:
State Of Biostar - Future Directions (January 2013)
biostars
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Istvan Albert
100k
25
votes
39
replies
5.8k
views
8 follow
Forum:
Bioinformatics Study Group
study-group
updated 14 months ago by
Ram
43k • written 10.8 years ago by
Olivier
▴ 440
226
votes
39
replies
288k
views
33 follow
Gene Id Conversion Tool
david
updated 6 months ago by
Ram
43k • written 14.5 years ago by
Renee
▴ 620
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 9 weeks ago by
nickp60
▴ 60 • written 7.9 years ago by
andrew.j.skelton73
6.6k
48
votes
38
replies
17k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
software
genome
annotation
updated 13 months ago by
Ram
43k • written 8.2 years ago by
Eric Normandeau
11k
39
votes
38
replies
9.0k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 21 months ago by
Ram
43k • written 8.5 years ago by
John
13k
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
Ram
43k • written 11.2 years ago by
Malachi Griffith
19k
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
Ram
43k • written 5.1 years ago by
Istvan Albert
100k
53
votes
38
replies
4.6k
views
10 follow
Multiple alignment software
alignment
clustal omega
tcoffee
updated 4.6 years ago by
Istvan Albert
100k • written 4.6 years ago by
juanjo75es
▴ 130
27
votes
38
replies
20k
views
Heatmap based with FPKM values
RNA-Seq
next-gen
R
updated 5.0 years ago by
Biostar
20 • written 6.5 years ago by
Mehmet
▴ 820
116,743 results • Page
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Answer: Does comparing two different groups to a common third group introduce bias in th
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Comment: High Malat-1 expression in single cell data
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C: Print Differentially Expressed Exons From Dexseq Results
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Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie
by
GenoMax
142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data
by
carolofharvest
▴ 30
Thank you for sharing. What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
Comment: Do I need to go back and filter my long-reads?
by
GenoMax
142k
> I think I will filter the reads ultimately. If your data was not run and basecalled using the same exact version of pore/software for a…
Comment: Raw counts using stringtie
by
Ram
43k
What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
Comment: Do I need to go back and filter my long-reads?
by
Ram
43k
> I think you should have the right to delete a question you yourself have submitted If you were to talk to someone, can you make them for…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★ 1.9k
I don't have any experience using `BRAKER2` so I cannot comment, but I would be extra careful about data you find on non-model organisms. T…
Comment: Differential Expression Analysis using DESeq2 in R
by
GenoMax
142k
You can copy and paste your code and then use `101010` button in the edit window to format it as text to keep it monospaced. For example …
Comment: Same sequencing sample in multiple lanes. How to analyse it?
by
ST
• 0
I guess this could really depend on the "counting" strategy, the library complexity and possible lane biases. If e.g., EM is used to guide…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
Vijith
▴ 30
Hi dthorbur, thanks for the response. I have run Augustus using Arabidopsis as a species. I would like to know about the suitability of usi…
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 6.0k
Alicia Oshlack has done some cool work on this but even the plots in her papers show that TPMs sometimes overcorrect and the relationship i…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![The below image contains the code and result also.][1] [1]: /media/images/96562b96-d508-4f67-96d1-7c71aa17
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