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
116,725 results • Page
1 of 2335
Sort: Views
Rank
Views
Votes
Replies
65
votes
3
replies
295k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 14 months ago by
Ram
43k • written 9.9 years ago by
Whoknows
▴ 960
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
279
votes
29
replies
284k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 17 months ago by
Ram
43k • written 11.5 years ago by
sohadb1357
▴ 640
334
votes
92
replies
240k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 9 months ago by
kalavattam
▴ 190 • written 13.3 years ago by
Biomed
5.0k
43
votes
24
replies
205k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 2.1 years ago by
matthew.pace
▴ 60 • written 10.4 years ago by
Arpitha Hebbar
▴ 210
12
votes
6
replies
201k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 3.7 years ago by
zx8754
11k • written 6.3 years ago by
hassanlou110
▴ 40
120
votes
31
replies
199k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Eric Normandeau
11k
62
votes
14
replies
196k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 12 months ago by
zx8754
11k • written 11.2 years ago by
Diana
▴ 910
288
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
131
votes
19
replies
183k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 3.0 years ago by
kajumi
• 0 • written 11.9 years ago by
shiy05
▴ 370
164
votes
8
replies
180k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 22 months ago by
Ram
43k • written 11.4 years ago by
lyz10302012
▴ 450
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
208
votes
21
replies
180k
views
12 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 17 months ago by
Istvan Albert
100k • written 13.5 years ago by
Andrea_Bio
★ 2.8k
124
votes
13
replies
174k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 8 months ago by
Ram
43k • written 13.8 years ago by
Biomed
5.0k
135
votes
18
replies
170k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 16 months ago by
katieostrouchov
▴ 30 • written 10.4 years ago by
timjoncooper
▴ 320
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
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
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
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 5 weeks ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
147
votes
31
replies
137k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 9 months ago by
Ram
43k • written 12.2 years ago by
Anima Mundi
★ 2.9k
10
votes
4
replies
134k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 12.8 years ago by
Stefano Berri
4.4k • written 12.8 years ago by
Don
▴ 20
13
votes
8
replies
130k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 19 months ago by
Ram
43k • written 12.5 years ago by
Zhshqzyc
▴ 520
68
votes
18
replies
130k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 3 months ago by
Pierre Lindenbaum
161k • written 9.6 years ago by
Kizuna
▴ 870
129
votes
32
replies
129k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 2.1 years ago by
Ram
43k • written 13.2 years ago by
Gon
▴ 540
166
votes
52
replies
128k
views
28 follow
Fastq Convert To Fasta
perl
10.5 years ago by
biolab
★ 1.4k
100
votes
9
replies
127k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 2.0 years ago by
henry-keen
▴ 40 • written 10.6 years ago by
newDNASeqer
▴ 760
23
votes
9
replies
127k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 14 months ago by
Ram
43k • written 9.0 years ago by
juan.rosas1
▴ 70
26
votes
10
replies
123k
views
Calculating P-Values From Z-Scores
statistics
r
updated 22 months ago by
Ram
43k • written 12.2 years ago by
Diana
▴ 910
119
votes
25
replies
123k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 7.2 years ago by
Hajk-Georg Drost
▴ 160 • written 13.8 years ago by
Biomed
5.0k
76
votes
26
replies
120k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 5 months ago by
cschu181
★ 2.8k • written 9.0 years ago by
Chenglin
▴ 260
3
votes
3
replies
119k
views
Find mismatch in two columns in a data frame in R
R
updated 8.2 years ago by
dan.shea
▴ 10 • written 8.2 years ago by
dirranrak
▴ 20
121
votes
7
replies
118k
views
Bam And Indexed Bam Files
bam
index
12.3 years ago by
Sahel
▴ 260
46
votes
10
replies
115k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 16 months ago by
Ram
43k • written 11.1 years ago by
biorepine
★ 1.5k
103
votes
34
replies
113k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 3 months ago by
Ram
43k • written 11.9 years ago by
GPR
▴ 390
115
votes
21
replies
113k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 12.1 years ago by
Aditya Joshi
▴ 30 • written 12.5 years ago by
Niek De Klein
★ 2.6k
105
votes
15
replies
112k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 6 weeks ago by
xiaoleiusc
▴ 140 • written 11.9 years ago by
GouthamAtla
12k
66
votes
9
replies
110k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 14 months ago by
Ram
43k • written 6.6 years ago by
Renesh
★ 2.2k
298
votes
33
replies
108k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
91
votes
10
replies
108k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 12.1 years ago by
Guangchuang Yu
★ 2.6k • written 12.1 years ago by
Wayne
★ 1.0k
65
votes
10
replies
107k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 3.7 years ago by
naloy
▴ 10 • written 5.6 years ago by
Sebastian Hesse
▴ 340
28
votes
8
replies
106k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 13.1 years ago by
User 5402
▴ 210
118
votes
15
replies
105k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 13.3 years ago by
Mona Mohamed
• 0 • written 13.5 years ago by
Terence
▴ 210
124
votes
56
replies
103k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 7 months ago by
William
▴ 30 • written 9.9 years ago by
kay
▴ 370
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
31
votes
8
replies
97k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java
structure
algorithm
updated 13.3 years ago by
Hazel
• 0 • written 14.0 years ago by
Hazel
▴ 70
85
votes
16
replies
97k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 17 months ago by
bhanu.chandra1
▴ 50 • written 9.1 years ago by
Prakki Rama
★ 2.7k
43
votes
8
replies
96k
views
samtools sorting and indexing
samtools
index
sort
updated 4.3 years ago by
onestop_data
▴ 330 • written 6.8 years ago by
ggman
▴ 90
239
votes
176
replies
95k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.8 years ago by
TriS
★ 4.7k
105
votes
31
replies
95k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 4 months ago by
mmfansler
▴ 450 • written 12.8 years ago by
2184687-1231-83-
★ 5.1k
116,725 results • Page
1 of 2335
Recent Votes
Answer: Download eQTL data of one specific gene for all tissues from GTEx
A: Tools To Calculate Average Coverage For A Bam File?
A: read depth using samtools
How to download raw sequence data from GEO/SRA
Tools To Calculate Average Coverage For A Bam File?
Recommend Your Favorite Bioinformatics Books
How Do You Manage Your Files & Directories For Your Projects ?
Recent Locations •
All
Ireland,
just now
United States,
1 minute ago
India,
2 minutes ago
United Kingdom,
2 minutes ago
United States,
3 minutes ago
Hanoi,
3 minutes ago
Palau,
4 minutes ago
Recent Awards •
All
Popular Question
to
yvonnehhe
• 0
Popular Question
to
curious
▴ 750
Scholar
to
jared.andrews07
★ 16k
Popular Question
to
hafiz.talhamalik
▴ 350
Popular Question
to
Hayler Edu
▴ 40
Popular Question
to
eesiribloom
▴ 80
Popular Question
to
g.persic1991
• 0
Recent Replies
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Can you try lowering the k to k=9? Wouldn't that mess with the results since all my kmers are 20bp? > You don't have any duplicate sequ…
Comment: Provean help
by
Mensur Dlakic
★ 27k
> Else, I will happy to send over the data and kindly perform the analysis for me. This website is meant to provide advice, not service. I…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you! Naive question, but does that list include all treatments in TCGA? I.e. is there anything missing from there, or that's it? Als…
Comment: Base Quality Score Recalibration with different reference genome
by
dtnondorf
• 0
Interesting! Thank you for such a quick response!
Comment: GATK genomicsDBimport intervals for WGS
by
Sd
• 0
I also have similar question. I sliced the genomic bed file with 50kb windows and 1kb padding into ~700 bed files; each bed file contains 9…
Comment: Base Quality Score Recalibration with different reference genome
by
GenoMax
142k
See answer here: https://www.biostars.org/p/9494503/#9494619 Heng Li said: https://twitter.com/lh3lh3/status/1410375781340135424 <!-- th…
Comment: DiffBind: no peaks in DBA
by
yvonneh
▴ 10
Ok fixed!
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
Can you try lowering the `k` to `k=9`? You don't have any duplicate sequences in your library file? That may be one reason why bbduk is r…
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
This topic is almost 5 years old, but I am facing the same (or at least a very similar) issue. I have ngs files from a CRISPR screen that …
Answer: RNA-seq data for deep learning classification
by
dsull
★ 5.9k
Honestly speaking, if it's deep learning, it probably doesn't matter that much if you use something like TPMs (probably not raw counts, unl…
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
Thanks for the detailed answer and I really appreciate it! I still have one question about why the number of reads can be influenced by the…
Comment: Split Fastq Files Into Chunks Of 1M Reads
by
thomas.heigl.ibk
• 0
i tried it. it splits, however, when i compare the first 8 lines of the second split file with the according lines from the original file, …
Comment: DiffBind: no peaks in DBA
by
Ram
43k
> I've also included the txt version of my .csv file No, you added a screenshot of plain text content, which is counterproductive. You can…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
At the GDC portal you have to turn the "therapeutic agents" toggle under "Clinical Data Analysis" on. ![drug][1] For Breast cancer you c…
Answer: Loss of 'var' using concatenation of AnnData objects
by
Hugo
• 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Traffic: 2705 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