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23,040 results • Page
1 of 461
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
281k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 7 months ago by
Ram
38k • written 13.4 years ago by
Renee
▴ 620
64
votes
3
replies
268k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 21 days ago by
Ram
38k • written 8.8 years ago by
Whoknows
▴ 960
267
votes
29
replies
251k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 4 months ago by
Ram
38k • written 10.4 years ago by
sohadb1357
▴ 610
319
votes
90
replies
214k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 6 months ago by
Ram
38k • written 12.2 years ago by
Biomed
4.8k
43
votes
24
replies
193k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 11 months ago by
matthew.pace
▴ 50 • written 9.3 years ago by
Arpitha Hebbar
▴ 210
151
votes
42
replies
174k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 10 months ago by
Ram
38k • written 11.1 years ago by
Obi Griffith
20k
276
votes
39
replies
164k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 3 days ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
188
votes
21
replies
163k
views
11 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 4 months ago by
Istvan Albert
97k • written 12.4 years ago by
Andrea_Bio
★ 2.8k
133
votes
18
replies
155k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 3 months ago by
katieostrouchov
▴ 20 • written 9.3 years ago by
timjoncooper
▴ 310
158
votes
8
replies
151k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 8 months ago by
Ram
38k • written 10.3 years ago by
lyz10302012
▴ 430
358
votes
79
replies
136k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 4 months ago by
Ram
38k • written 10.1 years ago by
ole.tange
★ 4.3k
223
votes
38
replies
134k
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 3 months ago by
harelarik
▴ 90 • written 10.1 years ago by
Malachi Griffith
19k
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
143
votes
30
replies
126k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 6 months ago by
Ram
38k • written 11.1 years ago by
Anima Mundi
★ 2.9k
129
votes
32
replies
122k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 11 months ago by
Ram
38k • written 12.1 years ago by
Gon
▴ 530
23
votes
9
replies
121k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 6 weeks ago by
Ram
38k • written 7.9 years ago by
juan.rosas1
▴ 70
26
votes
10
replies
120k
views
Calculating P-Values From Z-Scores
statistics
r
updated 9 months ago by
Ram
38k • written 11.1 years ago by
Diana
▴ 900
13
votes
8
replies
118k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 5 months ago by
Ram
38k • written 11.4 years ago by
Zhshqzyc
▴ 500
97
votes
9
replies
113k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 11 months ago by
henry-keen
▴ 40 • written 9.5 years ago by
newDNASeqer
▴ 750
46
votes
10
replies
112k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 3 months ago by
Ram
38k • written 10.0 years ago by
biorepine
★ 1.5k
730
votes
161
replies
108k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 13 days ago by
Biostar
1.6k • written 6.3 years ago by
Istvan Albert
97k
73
votes
25
replies
98k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 9 months ago by
Ram
38k • written 7.9 years ago by
Chenglin
▴ 250
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 23 days ago by
Genetics
▴ 20 • written 10.8 years ago by
GouthamAtla
12k
59
votes
9
replies
94k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 6 weeks ago by
Ram
38k • written 5.5 years ago by
Renesh
★ 2.1k
274
votes
33
replies
92k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 27 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
118
votes
53
replies
88k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 9 days ago by
Raag
• 0 • written 8.8 years ago by
kay
▴ 330
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
70
votes
16
replies
85k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna
samtools
mouse
updated 12 months ago by
Pierre Lindenbaum
153k • written 11.5 years ago by
Sakti
▴ 510
167
votes
41
replies
85k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 8 weeks ago by
Onur
• 0 • written 11.8 years ago by
Palu
▴ 240
238
votes
176
replies
84k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 5 months ago by
Ram
38k • written 7.7 years ago by
TriS
★ 4.6k
84
votes
16
replies
84k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 4 months ago by
bhanu.chandra1
▴ 50 • written 8.0 years ago by
Prakki Rama
★ 2.6k
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
79
votes
22
replies
81k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen
sequencing
fasta
rna
r
perl
updated 4 months ago by
Ram
38k • written 11.4 years ago by
Hamilton
▴ 290
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
70
votes
20
replies
80k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 11 weeks ago by
Ram
38k • written 12.4 years ago by
Unode
▴ 180
55
votes
11
replies
79k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq
fastq
updated 9 months ago by
Ram
38k • written 8.0 years ago by
catherine
▴ 220
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 6 months ago by
Ram
38k • written 13.0 years ago by
Yuri
★ 1.6k
136
votes
25
replies
75k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 11 months ago by
Ram
38k • written 10.9 years ago by
Ying W
★ 4.2k
157
votes
62
replies
74k
views
37 follow
Selecting Random Pairs From Fastq?
random
fastq
sequence
illumina
code
updated 9 months ago by
erin.baschal
• 0 • written 12.0 years ago by
Ketil
4.1k
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 14 days ago by
4galaxy77
2.6k • written 10.8 years ago by
Rubal7
▴ 820
16
votes
12
replies
73k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 7 months ago by
Luke
• 0 • written 8.4 years ago by
arronslacey
▴ 310
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
82
votes
21
replies
71k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 5 weeks ago by
cmdcolin
★ 2.9k • written 4.7 years ago by
otwtgin2010
▴ 540
67
votes
18
replies
69k
views
17 follow
Project For A Beginner Bioinformatics Student
project
java
updated 8 months ago by
Ram
38k • written 11.4 years ago by
And
▴ 230
33
votes
17
replies
69k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 9 weeks ago by
Ram
38k • written 11.8 years ago by
Fahmida
▴ 80
40
votes
14
replies
68k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 10 months ago by
Ram
38k • written 12.2 years ago by
Elena
▴ 250
194
votes
44
replies
68k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 11 weeks ago by
Ram
38k • written 10.5 years ago by
Obi Griffith
20k
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 6 months ago by
Ram
38k • written 12.4 years ago by
Zhangleisdau
▴ 340
59
votes
15
replies
67k
views
9 follow
BAM/SAM to FASTA conversion
sam
bam
updated 11 months ago by
Ram
38k • written 8.1 years ago by
biolab
★ 1.4k
74
votes
13
replies
65k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 4 months ago by
Ram
38k • written 9.4 years ago by
Nicholas Spies
★ 1.2k
23,040 results • Page
1 of 461
Recent Votes
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
smoothing or binning bigWig file
List of Ongoing and Planned Long Read Sequencing studies?
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Answer: Read lengths greater than insert length
A: Changing Output From Gene ID to Symbol When Running findMarkers from Scran
Answer: BLAST Database error: No alias or index file found for nucleotide database
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Recent Replies
Comment: split fasta file to train deep learning model
by
shenwei356
7.9k
Excluding sequences containing any letter not belonging to the 20 [amino acids letters](https://github.com/shenwei356/bio/blob/master/seq/a…
Comment: split fasta file to train deep learning model
by
pinheirofabiano
▴ 10
@shenwei356, thank you very much for your help, perfect! But now I realized that some fasta sequences contain the letter "B", which is ou…
Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
by
Mensur Dlakic
★ 23k
I think it depends on the speed of your local disks and the memory amount. On a single node, breaking up the database doesn't sound like a …
Comment: Sample size for population genetics
by
Jeremy Leipzig
21k
Other populations just make the model harder to generalize, not easier.
Comment: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
by
Vincent Laufer
★ 2.5k
i think there is some of that - my most upvoted comment of all time was a dismissive comment i made while extremely tired. for context i ha…
Comment: Molecular biologist / clinical pharmacologist (f/m/d)
by
Jeremy
▴ 770
Is this job on site in Vienna or remote?
Comment: smoothing or binning bigWig file
by
rls_08
▴ 40
if you use bigwigCompare , that would not create a sliding window, but instead, it will output the mean for each bin, according to the -bin…
Comment: Sample size for population genetics
by
zimmer.schweiz
• 0
Thank you so much for your answer. For common polygenic diseases, would it make sense to increase the number of populations sampled, in ord…
Answer: Sample size for population genetics
by
Jeremy Leipzig
21k
For a rare penetrant monogenic disease? A few cases. For a common polygenic disease or trait? 500k-10M
Answer: using GRanges metadata to constrain overlap searches between objects
by
seidel
11k
Rather than do all overlaps all the time for all samples, why not restrict the data by sample when you can. The code below works about 4 ti…
Comment: How to get gene from PSIBLAST resuts
by
Tom
• 0
Hello, thank you for your answer, I have a question, Why the information from the GFF file and from the feature table is different? I see …
Comment: SNP ID (rsID) to Chr no. and Position
by
Jewahir
• 0
Yeah, thank you for that!!
Comment: 1000 genomes hg38 with dbSNP rsid
by
Ram
38k
It should be pretty straightforward. Just to save you some pain, run these on the 1000g VCF once you download it: 1. `vt decompose -s` to …
Comment: 1000 genomes hg38 with dbSNP rsid
by
Vince
▴ 150
Yeah, I had some hope that I wouldn't need to mess with doing this ...
Answer: counting the unmapped reads
by
chemkhi.ali13
• 0
> Hi all, > > I have a sam file, my supervisor asked me to count the number of > unmapped reads, which command I should use? > > sam…
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