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Limit : this year
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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
131
votes
27
replies
40k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 11 months ago by
Ram
38k • written 10.9 years ago by
lh3
33k
130
votes
123
replies
28k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 9 hours ago by
krushnach80
★ 1.1k • written 4.4 years ago by
Kevin Blighe
84k
129
votes
32
replies
121k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 11 months ago by
Ram
38k • written 12.0 years ago by
Gon
▴ 530
127
votes
33
replies
53k
views
19 follow
VCF files: Change Chromosome Notation
vcf
next-gen
sequence
updated 4 months ago by
Ram
38k • written 8.9 years ago by
Quak
▴ 480
126
votes
44
replies
27k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 12 days ago by
Ram
38k • written 6.5 years ago by
Lars
▴ 970
122
votes
42
replies
8.7k
views
21 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 5 weeks ago by
Ram
38k • written 10.3 years ago by
Istvan Albert
97k
121
votes
44
replies
18k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 5 weeks ago by
Ram
38k • written 12.8 years ago by
Madelaine Gogol
5.3k
118
votes
26
replies
32k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq
Kallisto
RNASeq
Salmon
DESeq2
updated 12 days ago by
e.r.zakiev
▴ 30 • written 7.8 years ago by
mhockin
▴ 610
118
votes
53
replies
87k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 3 days ago by
Raag
• 0 • written 8.8 years ago by
kay
▴ 330
117
votes
59
replies
29k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware
next-gen
updated 6 weeks ago by
Ram
38k • written 7.9 years ago by
Angelo Victoria
▴ 30
116
votes
66
replies
40k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 8 days ago by
Ram
38k • written 4.7 years ago by
ATpoint
70k
116
votes
35
replies
7.0k
views
18 follow
Forum:
Is Biostar Killing The Bioinformatics Core?
core
biostars
updated 5 weeks ago by
Ram
38k • written 10.0 years ago by
Jeremy Leipzig
21k
116
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 4 months ago by
GenoMax
127k • written 12.3 years ago by
Casbon
★ 3.2k
116
votes
31
replies
35k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 9 months ago by
Ram
38k • written 9.6 years ago by
Eric Normandeau
11k
115
votes
35
replies
36k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
Forum
updated 11 days ago by
e.r.zakiev
▴ 30 • written 5.8 years ago by
ropolocan
▴ 760
112
votes
24
replies
45k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp
samtools
alignment
next-gen
sequencing
updated 6 months ago by
Ram
38k • written 11.9 years ago by
Matthieu
▴ 480
111
votes
25
replies
64k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 6 weeks ago by
Miguel
▴ 10 • written 12.1 years ago by
Pierre Lindenbaum
153k
110
votes
37
replies
6.9k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 5 weeks ago by
Ram
38k • written 11.5 years ago by
Pierre Lindenbaum
153k
109
votes
56
replies
40k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq
next-gen
sequencing
fusion
updated 6 months ago by
Ram
38k • written 10.8 years ago by
KS
▴ 380
106
votes
45
replies
80k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 6 months ago by
aswinssoman
▴ 20 • written 10.7 years ago by
Mchimich
▴ 320
106
votes
23
replies
20k
views
16 follow
Forum:
How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 19 days ago by
Ram
38k • written 9.1 years ago by
epigene
▴ 570
105
votes
46
replies
11k
views
13 follow
Forum:
Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 22 days ago by
Ram
38k • written 9.6 years ago by
ugly.betty77
★ 1.1k
105
votes
26
replies
38k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 5 months ago by
Ram
38k • written 10.2 years ago by
henryvuong
▴ 810
103
votes
12
replies
71k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 5 months ago by
Ram
38k • written 11.4 years ago by
Bioscientist
★ 1.7k
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
tool
updated 8 months ago by
Ram
38k • written 13.0 years ago by
Biostar User
★ 1.0k
102
votes
19
replies
17k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 29 days ago by
Ram
38k • written 10.8 years ago by
Anjan
▴ 830
102
votes
44
replies
7.7k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge
career
updated 22 days ago by
Ram
38k • written 9.6 years ago by
brentp
24k
101
votes
81
replies
24k
views
17 follow
Duplicates on Illumina
duplicates
illumina
updated 6 months ago by
GenoMax
127k • written 6.2 years ago by
predeus
★ 1.8k
100
votes
6
replies
22k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 7 days ago by
Ram
38k • written 4.6 years ago by
finswimmer
16k
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 17 days ago by
Genetics
▴ 20 • written 10.8 years ago by
GouthamAtla
12k
99
votes
21
replies
7.9k
views
14 follow
Forum:
How Has Bioinformatics Improved Over Time?
bioinformatics
updated 26 days ago by
Ram
38k • written 10.1 years ago by
Kate
▴ 370
99
votes
31
replies
81k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 8 months ago by
Ram
38k • written 11.7 years ago by
2184687-1231-83-
★ 5.0k
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 7 days ago by
Ram
38k • written 6.6 years ago by
Jean-Karim Heriche
26k
99
votes
36
replies
27k
views
32 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 8 weeks ago by
Jeremy Leipzig
21k • written 9.4 years ago by
14134125465346445
★ 3.6k
97
votes
9
replies
113k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 10 months ago by
henry-keen
▴ 40 • written 9.5 years ago by
newDNASeqer
▴ 750
97
votes
19
replies
87k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 7 months ago by
Ram
38k • written 13.1 years ago by
Giovanni M Dall'Olio
27k
97
votes
23
replies
32k
views
15 follow
Is Tophat The Only Mapper To Consider For Rna-Seq Data?
bwa
tophat
rna-seq
updated 10 months ago by
Ram
38k • written 10.2 years ago by
Lisa
▴ 330
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 27 days ago by
Ram
38k • written 10.5 years ago by
Istvan Albert
97k
94
votes
31
replies
37k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python
alignment
next-gen
sequencing
database
updated 11 months ago by
Ram
38k • written 12.6 years ago by
User 1586
▴ 280
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 9 days ago by
4galaxy77
2.6k • written 10.8 years ago by
Rubal7
▴ 820
93
votes
19
replies
55k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree
tool
phylogenetics
viewer
updated 10 months ago by
Theo
▴ 20 • written 12.5 years ago by
Niek De Klein
★ 2.6k
93
votes
50
replies
14k
views
17 follow
Forum:
Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics
23andMe
updated 20 days ago by
Ram
38k • written 9.3 years ago by
Istvan Albert
97k
92
votes
105
replies
34k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 8 days ago by
Ram
38k • written 4.6 years ago by
Kevin Blighe
84k
92
votes
46
replies
9.9k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 5 weeks ago by
Ram
38k • written 11.7 years ago by
Andra Waagmeester
3.2k
92
votes
20
replies
27k
views
13 follow
Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos
r
visualization
updated 10 months ago by
Ram
38k • written 11.1 years ago by
John
★ 1.5k
91
votes
20
replies
18k
views
15 follow
Forum:
Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing
N-of-one
WGS
RNA-Seq
next-gen
Exome
updated 5 months ago by
Ram
38k • written 8.8 years ago by
Obi Griffith
20k
91
votes
25
replies
57k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks
selection
software
updated 6 months ago by
Michael Dondrup
52k • written 12.1 years ago by
Jarretinha
3.4k
90
votes
38
replies
128k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 months ago by
Wang Cong
▴ 10 • written 10.7 years ago by
abi
▴ 370
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 11 months ago by
Ram
38k • written 11.9 years ago by
Ryan D
★ 3.4k
89
votes
19
replies
30k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 20 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
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Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
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Comment: Where do find virulence gene information in a gff/gtf file?
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Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
Ram
38k
Oh, you can just use TPM to do that. Within sample comparison is a completely different (and much easier) game.
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
Sian
• 0
Unfortunately yes, there does seem to be a problem with using the older version - when I came to do more analysis yesterday, the enrichKEGG…
Comment: getting coding exon information from Ensembl API
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▴ 30
Because you just answer when it's a stupid question or when I ask a lot of questions. This is for asking questions not for being judged by …
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
by
Manav
• 0
Thanks, tried working with the dataset and workflow. It worked.
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
BioinfoBee
• 0
@juke34 Thanks again. I changed the config.yaml *should overlapping loci (at CDS level) be merged in a single locus Only one gene is kept,…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
Thanks, I am not doing any differential. But, Can we say that 6th transcript is relatively more abundance in our sample than other transcri…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
zrm22
▴ 30
It looks like the ImputePipelinePlugin for the minimap2 run does not use the numThreads Option but rather does the numThreadsOnMachine - 2 …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
@rob Please, Can you or people from your group answer . As I am using one of your paper as my [reference.][1] [1]: https://f1000rese…
Comment: fastq_screen error: Failed to calculate read length
by
firestar
★ 1.5k
I created the .fasta from a BAM, so I am just going to go back to the BAM and convert that to a .fastq and see if that works. But good to k…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
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38k
> I have only one condition There is no "differential" then. RNAseq is a relative measure, so comparing single-condition replicates using …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
[Salmon][1] is giving me TPM at transcript level. So, What I understand from that TPM is normalized for sequencing depth and Transcript l…
Answer: Does it possible to know what are the adjacent genes up to 1000bp upstream and
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You could use `bedmap` from BEDOPS. Say you have a BED file of IS/transposable elements called `elements.bed` and a BED file of genes calle…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
twrl8
• 0
Ahh thank you! I thought the xmx parameter would be passed to the downstream commands called by the plugin. Then I think I definitely need…
Comment: mrbayes segmentation fault
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dgrace999
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Hello, Thank you. An explanation of where I came up with 2500 is 10 million divided by 1000 (because sample freq is 1000), divided again b…
Answer: How to extract proteins from PCs in plot_pca in DEP package?
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You can run PCA yourself with only few lines of code. See here under PCA https://www.biostars.org/p/461026/ You can then use the prcomp ou…
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