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116,694 results • Page
3 of 2334
Sort: replies
Rank
Views
Votes
Replies
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 13 months ago by
Ram
43k • written 5.3 years ago by
David Langenberger
11k
19
votes
43
replies
5.6k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by
nazaninhoseinkhan
▴ 520
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
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
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 22 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 9.5 years ago by
lh3
33k
11
votes
42
replies
4.1k
views
over presented kmer in fastq
fastqc
RNA-Seq
6.6 years ago by
Sam
▴ 150
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
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
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
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 12 months ago by
Ram
43k • written 7.7 years ago by
moxu
▴ 510
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
ivivek_ngs
★ 5.2k • written 6.7 years ago by
sophialovechan
▴ 80
38
votes
41
replies
60k
views
9 follow
Volcano Plot from DEseq2
R
written 6.5 years ago by
1769mkc
★ 1.2k
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
18
votes
41
replies
14k
views
6 follow
paired end illumina reads
Assembly
paired end
updated 21 months ago by
Ram
43k • written 8.5 years ago by
midox
▴ 290
5
votes
41
replies
2.9k
views
Insert sequence in nt database
nt
3.9 years ago by
anasofiamoreira94
▴ 80
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
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
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
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
31
votes
41
replies
2.7k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 10 months ago by
Ram
43k • written 4.2 years ago by
K.Gee
▴ 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
Ram
43k • written 9.5 years ago by
William
★ 5.3k
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 7.8 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
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
16
votes
40
replies
6.3k
views
About TCGA CNV data preprocessing
SNP
CNV
updated 5.5 years ago by
Kevin Blighe
87k • written 5.5 years ago by
Eric Wang
▴ 50
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
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
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
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
Ram
43k • written 9.7 years ago by
Obi Griffith
20k
55
votes
39
replies
5.8k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf
python
perl
awk
updated 11.6 years ago by
Rm
8.3k • written 11.7 years ago by
Mahdi Sarmady
▴ 310
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
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
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
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
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
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
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
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
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 8 weeks ago by
nickp60
▴ 60 • written 7.9 years ago by
andrew.j.skelton73
6.6k
39
votes
38
replies
9.0k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 20 months ago by
Ram
43k • written 8.5 years ago by
John
13k
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
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
Ram
43k • written 5.1 years ago by
Istvan Albert
100k
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
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 8.1 years ago by
Eric Normandeau
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
Ram
43k • written 11.2 years ago by
Malachi Griffith
19k
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 6.4 years ago by
Mehmet
▴ 820
116,694 results • Page
3 of 2334
Recent Votes
Answer: p-value in CIBERSORT
Answer: Can I have multiple active GDC download tokens?
Answer: Can I have multiple active GDC download tokens?
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Comment: Programmatically retrieving positions of protein active site residues
Comment: Programmatically retrieving positions of protein active site residues
Extracting genomic feature sequences from GTF/GFF files with AGAT
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Comment: Post-imputation plot
by
LChart
3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue
by
eleven11
• 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
Aspire
▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue
by
GenoMax
141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
Comment: KEGG Pathways
by
Ram
43k
Give us as much detail as you can. What error does it give you?
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 320
- `p.adjust()` is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, …
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
Comment: KEGG Pathways
by
Sudip
• 0
No it does not. Do you know of a way that can help me achieve what I want?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
GenoMax
141k
UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
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