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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Rox
★ 1.4k
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 5.2 years ago by
David Langenberger
11k
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
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
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
6.5 years ago by
Sam
▴ 150
8
votes
42
replies
4.7k
views
NaS (Nanopore Synthetic-long) help
Assembly
preprocessing
updated 15 months ago by
Ram
43k • written 8.9 years ago by
midox
▴ 290
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 12 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 10 days ago by
Jeremy Leipzig
22k • written 10.4 years ago by
14134125465346445
★ 3.6k
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 12.1 years ago by
Obi Griffith
20k
23
votes
41
replies
4.2k
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
6.1k
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
Ram
43k • written 7.6 years ago by
moxu
▴ 510
31
votes
41
replies
2.7k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 10 months ago by
Ram
43k • written 4.1 years ago by
K.Gee
▴ 40
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
16
votes
41
replies
9.5k
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
38
votes
41
replies
59k
views
9 follow
Volcano Plot from DEseq2
R
written 6.4 years ago by
1769mkc
★ 1.2k
5
votes
41
replies
2.8k
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
Ram
43k • written 6.9 years ago by
micro32uvas
▴ 10
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
18
votes
41
replies
3.3k
views
6 follow
Convert amino acid sequences into nucleotide sequences
nucleotide
protein
updated 4 months ago by
Joe
21k • written 6 months ago by
sil_bioinfo
▴ 40
171
votes
41
replies
97k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 6 months ago by
Ram
43k • written 12.8 years ago by
Palu
▴ 250
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 9.4 years ago by
William
★ 5.3k
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
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
6
votes
40
replies
11k
views
Fastx_Collapser Has No Fastq Output
fastx
RNA-seq
updated 13 months ago by
Ram
43k • written 10.6 years ago by
nbvasani
▴ 240
67
votes
40
replies
9.6k
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 9.4 years ago by
Gabriel R.
★ 2.9k
16
votes
40
replies
6.2k
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
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 7.5 years ago by
datascientist28
▴ 560
68
votes
40
replies
6.3k
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
10
votes
40
replies
6.5k
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
151
votes
39
replies
25k
views
20 follow
Forum:
A Farewell To Bioinformatics
bioinformatics
updated 14 months ago by
Ram
43k • written 11.2 years ago by
Martin A Hansen
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
Kumar
▴ 170 • written 12.3 years ago by
Amr
▴ 160
11
votes
39
replies
4.1k
views
Any advice for a de novo genome assembly
k-mer
de novo
genome
assembly
updated 7.4 years ago by
krsahlin
▴ 60 • written 7.4 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
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
Rm
8.3k • written 11.6 years ago by
Mahdi Sarmady
▴ 310
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
Ram
43k • written 5.0 years ago by
chernouhov sergey
▴ 50
25
votes
39
replies
5.8k
views
8 follow
Forum:
Bioinformatics Study Group
study-group
updated 13 months ago by
Ram
43k • written 10.8 years ago by
Olivier
▴ 440
81
votes
39
replies
7.5k
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
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 9.6 years ago by
Obi Griffith
20k
98
votes
39
replies
156k
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
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 6.4 years ago by
dhbradshaw
▴ 130
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
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
Ram
43k • written 14.1 years ago by
Marcos De Carvalho
▴ 310
78
votes
38
replies
32k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 7 weeks ago by
nickp60
▴ 60 • written 7.8 years ago by
andrew.j.skelton73
6.5k
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
Ram
43k • written 8.4 years ago by
John
13k
53
votes
38
replies
4.5k
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
48
votes
38
replies
17k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
software
genome
annotation
updated 12 months ago by
Ram
43k • written 8.1 years ago by
Eric Normandeau
11k
231
votes
38
replies
145k
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 11.1 years ago by
Malachi Griffith
19k
27
votes
38
replies
20k
views
Heatmap based with FPKM values
RNA-Seq
next-gen
R
updated 4.9 years ago by
Biostar
20 • written 6.4 years ago by
Mehmet
▴ 820
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 24 months ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
129
votes
38
replies
8.1k
views
21 follow
Forum:
Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 10 months ago by
Ram
43k • written 5.0 years ago by
Istvan Albert
100k
1,000 results • Page
3 of 20
Recent Votes
Answer: Filtration Of Reads With Length Lower Than 30 From Bam
Answer: How to compare the quality of assemblies
Comment: How to compare the quality of assemblies
Bedtools merge but only if intersection exists
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
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Recent Replies
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
• 0
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR.
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
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