Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
276k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 6 days ago by
Ram
36k • written 12.8 years ago by
Renee
▴ 620
58
votes
3
replies
248k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
expression
gene
Tutorial
RNA-Seq
protein
updated 10 months ago by
Ram
36k • written 8.2 years ago by
Whoknows
▴ 900
262
votes
30
replies
231k
views
24 follow
How To Filter Mapped Reads With Samtools
samtools
updated 5 weeks ago by
Ram
36k • written 9.8 years ago by
sohadb1357
▴ 610
315
votes
89
replies
200k
views
56 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 22 days ago by
SplitInf
▴ 10 • written 11.6 years ago by
Biomed
4.8k
43
votes
24
replies
185k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 4 months ago by
matthew.pace
▴ 30 • written 8.7 years ago by
Arpitha Hebbar
▴ 210
59
votes
12
replies
173k
views
7 follow
How To Deal With Duplicate Row Names Error In R
r
updated 8 months ago by
Ram
36k • written 9.5 years ago by
Diana
▴ 900
151
votes
42
replies
170k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 3 months ago by
Ram
36k • written 10.5 years ago by
Obi Griffith
20k
120
votes
19
replies
165k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 15 months ago by
kajumi
• 0 • written 10.2 years ago by
shiy05
▴ 340
12
votes
6
replies
163k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 23 months ago by
zx8754
11k • written 4.6 years ago by
hassanlou110
▴ 40
138
votes
14
replies
159k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 2.7 years ago by
Renesh
★ 2.1k • written 12.4 years ago by
Pierre Lindenbaum
148k
118
votes
31
replies
155k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta
parsing
python
updated 10 months ago by
GenoMax
119k • written 12.3 years ago by
Eric Normandeau
11k
181
votes
19
replies
155k
views
9 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 11.6 years ago by
Neilfws
49k • written 11.8 years ago by
Andrea_Bio
★ 2.8k
271
votes
39
replies
153k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
download
GEO
bam
updated 3 months ago by
Ram
36k • written 8.0 years ago by
Obi Griffith
20k
121
votes
11
replies
149k
views
11 follow
How Can I Convert Bam To Sam?
next-gen
sequencing
bam
sam
conversion
updated 11 months ago by
t.montserrat.ayuso
• 0 • written 12.1 years ago by
Biomed
4.8k
126
votes
19
replies
145k
views
14 follow
Blast - Formatting Output
blast
format
output
updated 23 months ago by
apekshasharma7777
• 0 • written 8.7 years ago by
timjoncooper
▴ 300
147
votes
8
replies
133k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 5 weeks ago by
Ram
36k • written 9.7 years ago by
lyz10302012
▴ 390
353
votes
80
replies
132k
views
32 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
next-gen
parallel
ngs
Tool
tools
updated 4 months ago by
Ram
36k • written 9.5 years ago by
ole.tange
★ 4.2k
10
votes
4
replies
129k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 11.1 years ago by
Stefano Berri
4.3k • written 11.1 years ago by
Don
▴ 20
219
votes
36
replies
127k
views
27 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 5 months ago by
jena
▴ 200 • written 9.5 years ago by
Malachi Griffith
19k
26
votes
10
replies
118k
views
Calculating P-Values From Z-Scores
statistics
r
updated 8 weeks ago by
Ram
36k • written 10.5 years ago by
Diana
▴ 900
129
votes
32
replies
118k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 4 months ago by
Ram
36k • written 11.5 years ago by
Gon
▴ 530
23
votes
9
replies
117k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 6.0 years ago by
Vasei
▴ 30 • written 7.3 years ago by
juan.rosas1
▴ 70
139
votes
30
replies
117k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 14 months ago by
jena
▴ 200 • written 10.5 years ago by
Anima Mundi
★ 2.9k
114
votes
25
replies
115k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 5.5 years ago by
Hajk-Georg Drost
▴ 160 • written 12.1 years ago by
Biomed
4.8k
81
votes
37
replies
113k
views
17 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 13 months ago by
kperlejewski
• 0 • written 10.1 years ago by
abi
▴ 370
13
votes
8
replies
110k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 5 weeks ago by
Ram
36k • written 10.8 years ago by
Zhshqzyc
▴ 490
115
votes
21
replies
110k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 10.4 years ago by
Aditya Joshi
▴ 30 • written 10.8 years ago by
Niek De Klein
★ 2.6k
158
votes
52
replies
109k
views
28 follow
Fastq Convert To Fasta
perl
8.8 years ago by
biolab
★ 1.4k
3
votes
3
replies
109k
views
Find mismatch in two columns in a data frame in R
R
updated 6.4 years ago by
dan.shea
▴ 10 • written 6.4 years ago by
dirranrak
▴ 20
46
votes
10
replies
108k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 2.7 years ago by
Renesh
★ 2.1k • written 9.4 years ago by
biorepine
★ 1.5k
95
votes
10
replies
104k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 3 months ago by
henry-keen
▴ 30 • written 8.9 years ago by
newDNASeqer
▴ 750
28
votes
8
replies
104k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 11.4 years ago by
User 5402
▴ 210
91
votes
10
replies
104k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 10.4 years ago by
Guangchuang Yu
★ 2.5k • written 10.4 years ago by
Wayne
★ 1.0k
118
votes
15
replies
99k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 11.6 years ago by
Mona Mohamed
• 0 • written 11.8 years ago by
Terence
▴ 210
112
votes
7
replies
99k
views
Bam And Indexed Bam Files
bam
index
10.6 years ago by
Sahel
▴ 240
31
votes
8
replies
95k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java
structure
algorithm
updated 11.6 years ago by
Hazel
• 0 • written 12.3 years ago by
Hazel
▴ 70
692
votes
160
replies
93k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
970 • written 5.7 years ago by
Istvan Albert
94k
61
votes
16
replies
92k
views
11 follow
from .BAM to .BAI using samtools
sequencing
samtools
next-gen
updated 6 months ago by
Ram
36k • written 7.9 years ago by
Kizuna
▴ 860
93
votes
14
replies
89k
views
14 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 4 months ago by
Juke34
7.2k • written 10.2 years ago by
GouthamAtla
12k
59
votes
9
replies
87k
views
8 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
RNA-Seq
Blog
gene
expression
12 months ago by
Renesh
★ 2.1k
86
votes
31
replies
87k
views
20 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 5 months ago by
lidan0001
▴ 50 • written 10.2 years ago by
GPR
▴ 380
172
votes
30
replies
86k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 6 months ago by
Ram
36k • written 11.3 years ago by
Ct586
▴ 600
270
votes
33
replies
84k
views
24 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
tutorial
Tutorial
updated 6 months ago by
tshtatland
▴ 100 • written 8.8 years ago by
Obi Griffith
20k
71
votes
25
replies
84k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 6 weeks ago by
Ram
36k • written 7.3 years ago by
Chenglin
▴ 230
93
votes
19
replies
84k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 6 days ago by
Ram
36k • written 12.5 years ago by
Giovanni M Dall'Olio
27k
43
votes
15
replies
82k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna
edger
r
counts
updated 7.7 years ago by
seidel
9.5k • written 11.4 years ago by
Jason
▴ 910
65
votes
16
replies
80k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna
samtools
mouse
updated 4 months ago by
Pierre Lindenbaum
148k • written 10.9 years ago by
Sakti
▴ 500
112
votes
52
replies
80k
views
21 follow
How to plot coverage and depth statistics of a bam file
sequencing
coverage
bam
depth
next-gen
updated 20 days ago by
poet1988
• 0 • written 8.2 years ago by
kay
▴ 310
234
votes
176
replies
79k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 4 weeks ago by
Ram
36k • written 7.0 years ago by
TriS
★ 4.6k
35
votes
8
replies
79k
views
samtools sorting and indexing
samtools
index
sort
updated 2.6 years ago by
onestop_data
▴ 300 • written 5.1 years ago by
ggman
▴ 80
1,000 results • Page
1 of 20
Recent Votes
Answer: Changing the x-axis in ggseqlogo in R
Answer: Installing ensembl-vep
Answer: Installing ensembl-vep
Answer: Changing the x-axis in ggseqlogo in R
Answer: Best way to detect CNV using WGS data
Best way to detect CNV using WGS data
Answer: Concatenate information columns from multiple identical bed files.
Recent Locations •
All
France/Nantes/Institut du Thorax - INSERM UMR1087,
just now
United States,
1 minute ago
Cambridge, MA,
1 minute ago
Boston,
1 minute ago
United States,
2 minutes ago
London,
2 minutes ago
Japan,
2 minutes ago
Recent Awards •
All
Teacher
to
GouthamAtla
12k
Popular Question
to
fifty_fifty
▴ 30
Popular Question
to
tothepoint
▴ 680
Popular Question
to
Hansen_869
▴ 40
Popular Question
to
nitishd.dave
▴ 20
Teacher
to
Mensur Dlakic
★ 20k
Popular Question
to
edsouza
▴ 30
Recent Replies
Comment: using gatk haplotypecaller for variants extraction
by
Nemo
• 0
thanks @Ram, yes I searched for my question, and I read the link you sent. As I found I can use gatk haplotypecaller (I am skeptical yet) b…
Comment: How to deal with `'select()' returned 1:many mapping between keys and columns` w
by
LChart
640
> Is it because some genes do not have entrez ID? Yes. > If so, how should I deal with it? If you strictly require entrez IDs, then you…
Comment: using gatk haplotypecaller for variants extraction
by
Ram
36k
> I see the sample commands but I noticed they are for DNA seq data. So, it means I cannot use gatk haplotypecaller for rna seq data? You…
Comment: How to use RSEM to quantify genes and transcript expression from STAR outpute fi
by
Ram
36k
The "what is this supposed to be" part is the output prefix. Are you using `>&` when you mean to use `&>`? In any case, use `>rsem.out 2>rs…
Comment: Gene-based and transcriptome-based profiling
by
GenoMax
119k
It may be a case of semantics. When arrays were popular in early 2000s, people used the term "gene-based profiling". Both cases one is look…
Comment: Changing the x-axis in ggseqlogo in R
by
Ram
36k
I've moved the comment to an answer. Please accept it to mark the post as solved.
Comment: Changing the x-axis in ggseqlogo in R
by
margo
▴ 40
Thank you! That works!
Answer: Changing the x-axis in ggseqlogo in R
by
rpolicastro
9.4k
Untested but adding `+ scale_x_continuous(breaks=1:21, labels=-10:10)` to the returned ggplot2 object should work.
Answer: Installing ensembl-vep
by
tomas4482
▴ 300
You can either create a new environment using Anaconda3 and download it via `conda install -n vep -c bioconda ensembl-vep` or install every…
Comment: Gene-based and transcriptome-based profiling
by
Chris
• 0
Thank you so much for detailed answer! I am not confused about transcriptome-base profiling because I think it is RNA-Seq analysis. I only …
Answer: Concatenate information columns from multiple identical bed files.
by
Trivas
▴ 480
If you're comfortable using R, you can load the `.bed` files as tab delimited files, then `full_join` using `chr`, `start`, and `stop` as y…
Comment: Gene types to use for RNA counts case-control
by
i.sudbery
15k
Its not that we don't know which transcripts are poly-adenylated and which arn't - its just that that information is not encoded in the gen…
Comment: Gene types to use for RNA counts case-control
by
i.sudbery
15k
DESeq2 automatically removes low expression genes, no? And it does that by picking the the expression threshold that maximises the number …
Comment: Impute genotype probabilities with BEAGLE
by
dario.galanti92
• 0
Well, all those SNPs are missing in the first individual (TA_AM_01_01_F3_CC0_M1_1) in the input (GT --> "./.") and they are imputed and gen…
Comment: How many reads will be removed after markduplicates in general?
by
Sashu
▴ 10
Returning to the original question, would you think it's strange that the depth of bulk DNA-seq data decreases too much after markduplicat…
Traffic: 1745 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6