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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
28
votes
42
replies
5.1k
views
7 follow
How to add tophat and bowtie to the path?
export PATH
bowtie2.2.9
tophat2
6.1 years ago by
mirza
▴ 180
19
votes
41
replies
6.8k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 5.4 years ago by
ivivek_ngs
★ 5.2k • written 5.4 years ago by
sophialovechan
▴ 70
78
votes
41
replies
27k
views
24 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 9 weeks ago by
Acadia
• 0 • written 9.3 years ago by
Irsan
★ 7.6k
5
votes
41
replies
1.7k
views
Insert sequence in nt database
nt
2.7 years ago by
anasofiamoreira94
▴ 80
202
votes
41
replies
23k
views
20 follow
Forum:
Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics
cram
gatk
galaxy
updated 10 months ago by
Ram
37k • written 8.2 years ago by
William
★ 5.1k
98
votes
41
replies
4.3k
views
17 follow
Forum:
I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software error
sequencing
next-gen
Forum
updated 6.4 years ago by
Istvan Albert
96k • written 6.4 years ago by
moxu
▴ 500
16
votes
41
replies
7.6k
views
How to extract information from headers of fasta file
sequence
updated 7 months ago by
Ram
37k • written 7.9 years ago by
Crystal
▴ 70
59
votes
41
replies
18k
views
16 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow
pbalign
pacbio
polishing
smrt limk
Tutorial
updated 2.7 years ago by
zjl1983
• 0 • written 5.4 years ago by
Rox
★ 1.4k
135
votes
41
replies
20k
views
20 follow
Forum:
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Forum
updated 9.3 years ago by
always_learning
★ 1.1k • written 9.6 years ago by
Whetting
★ 1.6k
18
votes
41
replies
10k
views
6 follow
paired end illumina reads
Assembly
paired end
updated 6 months ago by
Ram
37k • written 7.3 years ago by
midox
▴ 290
13
votes
41
replies
1.5k
views
Is my file created completely
sam file
BWA MEM
updated 5.7 years ago by
h.mon
34k • written 5.7 years ago by
micro32uvas
▴ 10
31
votes
41
replies
1.3k
views
12 follow
Forum:
Question regarding journal publications
journals
publications
Forum
2.9 years ago by
K.Gee
▴ 40
38
votes
41
replies
46k
views
9 follow
Volcano Plot from DEseq2
R
written 5.2 years ago by
krushnach80
★ 1.1k
23
votes
41
replies
12k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 10 weeks ago by
lovelymaoqin
• 0 • written 5.0 years ago by
BrunoGiotti
▴ 110
17
votes
40
replies
15k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
run
easy
orthomcl
all-v-all
mcl
Tutorial
updated 2.2 years ago by
Buffo
★ 2.0k • written 6.6 years ago by
Esaie
▴ 160
40
votes
40
replies
9.0k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq
alignment
updated 4.9 years ago by
Kevin Blighe
84k • written 6.3 years ago by
datascientist28
▴ 520
68
votes
40
replies
4.7k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen
sequencing
sequencing
updated 11.3 years ago by
pmenzel
▴ 310 • written 11.3 years ago by
Samuel Lampa
★ 1.3k
16
votes
40
replies
4.6k
views
About TCGA CNV data preprocessing
SNP
CNV
updated 4.3 years ago by
Kevin Blighe
84k • written 4.3 years ago by
Eric Wang
▴ 40
67
votes
40
replies
8.0k
views
12 follow
Forum:
I want to re-open the old debate: python or perl ?
perl
python
updated 11 months ago by
Ram
37k • written 8.2 years ago by
Gabriel R.
★ 2.9k
10
votes
40
replies
4.8k
views
weird insert size post trimming
RNA-Seq
updated 5.4 years ago by
Gabriel R.
★ 2.9k • written 5.5 years ago by
badribio
▴ 280
6
votes
40
replies
8.9k
views
Fastx_Collapser Has No Fastq Output
bioinformatics
fastx
rna-seq
updated 6.3 years ago by
cedric.laczny
▴ 50 • written 9.4 years ago by
nbvasani
▴ 240
151
votes
39
replies
22k
views
20 follow
Forum:
A Farewell To Bioinformatics
bioinformatics
Forum
updated 5.3 years ago by
Kevin Blighe
84k • written 10.0 years ago by
Martin A Hansen
3.0k
20
votes
39
replies
7.6k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast
blast
memory
updated 7.4 years ago by
Kumar
▴ 150 • written 11.0 years ago by
Amr
▴ 160
25
votes
39
replies
4.4k
views
8 follow
Forum:
Bioinformatics Study Group
bioinformatics
Forum
9.5 years ago by
Olivier
▴ 440
55
votes
39
replies
4.4k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf
python
perl
awk
updated 10.4 years ago by
Rm
8.2k • written 10.4 years ago by
Mahdi Sarmady
▴ 310
18
votes
39
replies
2.7k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
Tool
C++
tool
c++
22 months ago by
chernouhov sergey
▴ 50
69
votes
39
replies
3.2k
views
14 follow
Forum:
Preparation for Bioinformatics.SE closing
biostars
Forum
updated 5.7 years ago by
me
▴ 750 • written 5.7 years ago by
John
13k
81
votes
39
replies
5.9k
views
11 follow
News:
State Of Biostar - Future Directions (January 2013)
biostar
News
updated 10.0 years ago by
João Rodrigues
★ 2.5k • written 10.1 years ago by
Istvan Albert
96k
36
votes
39
replies
2.6k
views
11 follow
Forum:
Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
RNA-Seq
alignment
blast
next-gen
sequencing
Forum
updated 5.2 years ago by
Puli Chandramouli Reddy
▴ 190 • written 5.2 years ago by
dhbradshaw
▴ 130
11
votes
39
replies
2.8k
views
Any advice for a de novo genome assembly
k-mer
de novo
genome
assembly
updated 6.2 years ago by
krsahlin
▴ 60 • written 6.2 years ago by
Picasa
▴ 630
66
votes
39
replies
6.2k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career
subjective
updated 22 months ago by
Ram
37k • written 12.9 years ago by
Marcos De Carvalho
▴ 310
226
votes
39
replies
279k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 5 months ago by
Ram
37k • written 13.3 years ago by
Renee
▴ 620
273
votes
39
replies
161k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
download
GEO
bam
updated 9 months ago by
Ram
37k • written 8.4 years ago by
Obi Griffith
20k
39
votes
38
replies
6.8k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 5 months ago by
Ram
37k • written 7.2 years ago by
John
13k
53
votes
38
replies
3.2k
views
10 follow
Multiple alignment software
alignment
clustal omega
tcoffee
updated 3.4 years ago by
Istvan Albert
96k • written 3.4 years ago by
juanjo75es
▴ 130
129
votes
38
replies
5.4k
views
21 follow
Forum:
Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
Forum
updated 3.8 years ago by
Alex Reynolds
34k • written 3.8 years ago by
Istvan Albert
96k
220
votes
38
replies
132k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 6 weeks ago by
harelarik
▴ 90 • written 9.9 years ago by
Malachi Griffith
19k
26
votes
38
replies
16k
views
Heatmap based with FPKM values
RNA-Seq
next-gen
R
updated 3.7 years ago by
Biostar
20 • written 5.2 years ago by
Mehmet
▴ 780
164
votes
38
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
written 11.6 years ago by
Palu
▴ 240
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 9 months ago by
Ram
37k • written 8.0 years ago by
Mo
▴ 920
48
votes
38
replies
15k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
genome
annotation
software
Forum
updated 6.9 years ago by
Jon
▴ 360 • written 6.9 years ago by
Eric Normandeau
11k
89
votes
38
replies
123k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 4 months ago by
Wang Cong
▴ 10 • written 10.6 years ago by
abi
▴ 370
159
votes
38
replies
14k
views
22 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
bioinformatics
Forum
humor
updated 4 months ago by
Ambu Vijayan
▴ 30 • written 9.8 years ago by
Istvan Albert
96k
47
votes
37
replies
7.1k
views
12 follow
Forum:
The Organisation Of Really Contrived Acronyms (Orca)
Forum
updated 9.4 years ago by
Jeremy Leipzig
21k • written 9.4 years ago by
Niallhaslam
2.3k
29
votes
37
replies
2.3k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf
ped
phased
4.2 years ago by
Shicheng Guo
★ 9.2k
17
votes
37
replies
3.1k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.7 years ago by
Biostar
20 • written 3.8 years ago by
williamsbrian5064
▴ 470
43
votes
37
replies
1.5k
views
7 follow
Forum:
Checking the quality and reliability in bioinformatics
bioinformatics
Forum
updated 5.3 years ago by
WouterDeCoster
47k • written 5.3 years ago by
fi1d18
★ 4.1k
18
votes
37
replies
11k
views
11 follow
Is it possible to download the full EpiCov database from GISAID?
GISAID
genome
Database
EpiCoV
updated 21 months ago by
jena
▴ 240 • written 2.9 years ago by
dgarcia54
▴ 30
130
votes
37
replies
11k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 11.4 years ago by
Pals
★ 1.3k • written 11.4 years ago by
Sirus
▴ 820
16
votes
37
replies
14k
views
7 follow
extracting the soft clipped seq only from a sam file
sam
bam
soft clip
updated 6.5 years ago by
Biostar
20 • written 8.1 years ago by
Varun Gupta
★ 1.2k
1,000 results • Page
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Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
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Answer: trainGlimmerHMM Error while training a genome
by
congliu37
• 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
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I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
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Thank you FrankStarling, ATpoint, jv, these were so helpful.
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> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
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vvasta
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I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
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but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
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★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
by
Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
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152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4
by
Pierre Lindenbaum
152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of gzip < chr1.vcf.gz > chr1.vcf.gz…
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**Error: unable to open file or unable to determine types for file** Hi i am trying to run this commands **bedtools intersect -a Ec_k1…
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by
Asan Emirsale
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You should find complementary sequences to make the miRNA silent. Should it be the Biopython or another tool. The solution might be as simp…
Comment: counting reads in a fastq file using a refrence fasta file
by
vaslanzadeh
▴ 10
Thanks, this works but it is extremely slow, is there any other alternatives?
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