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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
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
267
votes
29
replies
246k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 10 weeks ago by
Ram
37k • written 10.3 years ago by
sohadb1357
▴ 610
318
votes
90
replies
210k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 4 months ago by
Ram
37k • written 12.0 years ago by
Biomed
4.8k
43
votes
24
replies
191k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 10 months ago by
matthew.pace
▴ 40 • written 9.2 years ago by
Arpitha Hebbar
▴ 210
151
votes
42
replies
173k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 8 months ago by
Ram
37k • written 10.9 years ago by
Obi Griffith
20k
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
188
votes
21
replies
161k
views
11 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 11 weeks ago by
Istvan Albert
96k • written 12.2 years ago by
Andrea_Bio
★ 2.8k
131
votes
18
replies
152k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 7 weeks ago by
katieostrouchov
▴ 20 • written 9.1 years ago by
timjoncooper
▴ 310
158
votes
8
replies
146k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 6 months ago by
Ram
37k • written 10.1 years ago by
lyz10302012
▴ 430
358
votes
79
replies
135k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 10 weeks ago by
Ram
37k • written 10.0 years ago by
ole.tange
★ 4.3k
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 7 weeks ago by
harelarik
▴ 90 • written 9.9 years ago by
Malachi Griffith
19k
89
votes
38
replies
124k
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
140
votes
30
replies
124k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 4 months ago by
Ram
37k • written 11.0 years ago by
Anima Mundi
★ 2.9k
129
votes
32
replies
121k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 10 months ago by
Ram
37k • written 11.9 years ago by
Gon
▴ 530
26
votes
10
replies
120k
views
Calculating P-Values From Z-Scores
statistics
r
updated 7 months ago by
Ram
37k • written 11.0 years ago by
Diana
▴ 900
13
votes
8
replies
116k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 4 months ago by
Ram
37k • written 11.2 years ago by
Zhshqzyc
▴ 490
46
votes
10
replies
111k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 7 weeks ago by
Ram
37k • written 9.8 years ago by
biorepine
★ 1.5k
97
votes
9
replies
111k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 9 months ago by
henry-keen
▴ 40 • written 9.4 years ago by
newDNASeqer
▴ 750
715
votes
159
replies
104k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
1.5k • written 6.2 years ago by
Istvan Albert
96k
98
votes
14
replies
95k
views
14 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 10 months ago by
Juke34
7.5k • written 10.7 years ago by
GouthamAtla
12k
72
votes
25
replies
94k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 7 months ago by
Ram
37k • written 7.8 years ago by
Chenglin
▴ 250
93
votes
31
replies
94k
views
20 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 11 months ago by
Dan
▴ 60 • written 10.7 years ago by
GPR
▴ 380
97
votes
19
replies
86k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 5 months ago by
Ram
37k • written 13.0 years ago by
Giovanni M Dall'Olio
27k
115
votes
52
replies
85k
views
21 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 3 days ago by
Ram
37k • written 8.6 years ago by
kay
▴ 320
70
votes
16
replies
84k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna
samtools
mouse
updated 10 months ago by
Pierre Lindenbaum
152k • written 11.4 years ago by
Sakti
▴ 510
166
votes
41
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 4 days ago by
Onur
• 0 • written 11.6 years ago by
Palu
▴ 240
234
votes
176
replies
83k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 3 months ago by
Ram
37k • written 7.5 years ago by
TriS
★ 4.6k
83
votes
16
replies
82k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 10 weeks ago by
bhanu.chandra1
▴ 50 • written 7.8 years ago by
Prakki Rama
★ 2.6k
97
votes
31
replies
79k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 6 months ago by
Ram
37k • written 11.6 years ago by
2184687-1231-83-
★ 5.0k
79
votes
22
replies
79k
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 10 weeks ago by
Ram
37k • written 11.3 years ago by
Hamilton
▴ 290
106
votes
45
replies
79k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 5 months ago by
aswinssoman
▴ 20 • written 10.5 years ago by
Mchimich
▴ 320
70
votes
20
replies
79k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 28 days ago by
Ram
37k • written 12.2 years ago by
Unode
▴ 180
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 5 months ago by
Ram
37k • written 12.9 years ago by
Yuri
★ 1.6k
55
votes
11
replies
77k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq
fastq
updated 8 months ago by
Ram
37k • written 7.9 years ago by
catherine
▴ 220
136
votes
25
replies
74k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 10 months ago by
Ram
37k • written 10.8 years ago by
Ying W
★ 4.2k
157
votes
62
replies
73k
views
37 follow
Selecting Random Pairs From Fastq?
random
fastq
sequence
illumina
code
updated 7 months ago by
erin.baschal
• 0 • written 11.9 years ago by
Ketil
4.1k
92
votes
24
replies
72k
views
19 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 12 months ago by
ashotmarg2004
▴ 120 • written 10.7 years ago by
Rubal7
▴ 820
15
votes
12
replies
71k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 5 months ago by
Luke
• 0 • written 8.3 years ago by
arronslacey
▴ 310
103
votes
12
replies
70k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 3 months ago by
Ram
37k • written 11.3 years ago by
Bioscientist
★ 1.7k
122
votes
17
replies
69k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping
genome
updated 10 months ago by
Ram
37k • written 11.8 years ago by
Nick
▴ 370
33
votes
17
replies
68k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 15 days ago by
Ram
37k • written 11.7 years ago by
Fahmida
▴ 80
67
votes
18
replies
68k
views
17 follow
Project For A Beginner Bioinformatics Student
project
java
updated 6 months ago by
Ram
37k • written 11.2 years ago by
And
▴ 230
40
votes
14
replies
68k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 9 months ago by
Ram
37k • written 12.1 years ago by
Elena
▴ 250
76
votes
19
replies
68k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools
bcftools
htslib
Tutorial
updated 12 days ago by
jcurry01
• 0 • written 4.5 years ago by
otwtgin2010
▴ 520
194
votes
44
replies
67k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 25 days ago by
Ram
37k • written 10.4 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 4 months ago by
Ram
37k • written 12.3 years ago by
Zhangleisdau
▴ 340
59
votes
15
replies
66k
views
9 follow
BAM/SAM to FASTA conversion
sam
bam
updated 9 months ago by
Ram
37k • written 8.0 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 3 months ago by
Ram
37k • written 9.2 years ago by
Nicholas Spies
★ 1.2k
40
votes
15
replies
64k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix
conversion
entrez
updated 4 months ago by
Ram
37k • written 9.6 years ago by
Josh
▴ 140
35
votes
9
replies
63k
views
8 follow
Minor allele frequency calculation
SNP
next-gen
updated 8 months ago by
Ram
37k • written 8.2 years ago by
Tark
▴ 50
1,000 results • Page
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Over Representation Vs Enrichment Analysis
Answer: Using Seurat function `FindMarkers` to find differentially expressed genes betwe
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Answer: Remove mitochondrial reads from BAM files
Comment: translate CDS to prot formatted with nt nubers
Comment: Analyzing bulk RNA-seq
Comment: Analyzing bulk RNA-seq
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Comment: Diffbind losing peaks when going from small to larger consensus peak set
by
tara.mcintyre
• 0
I'm now realizing it might be due to the filter parameter being set =1 when I run dba.count because when I set it to 0, all of the peaks ar…
Answer: Obtaining every"Protein ID" from a genome in OMA
by
clement.train
▴ 40
Hello, It seems that the current download is limited to 100 genes on the genomes pages, we will increase this limit to the extent of ea…
Comment: DNA methylation (RRBS/WGBS) prediction from DNA sequence (WGS)
by
Lalaland
▴ 10
Thank you very much, Matthias! I will definitely check those links out myself!
Comment: RNA Editing data from RNA-seq
by
Juke34
7.5k
What tool did you look at ?
Comment: want the codes for Deseq2 to perform DEGs.
by
rupali
• 0
thanks for help
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
by
Yingying
• 0
Hi, Yes I've uploaded the diagnostic file to 10x support already, but haven't got any response yet.
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
by
GenoMax
125k
You may want to contact 10x tech support. When this process failed it must have created a diagnostic archive. You also get a message about …
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
by
jv
▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs
by
schlogl
▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10
by
ATpoint
68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file
by
ibq.enriquepola
• 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
by
Chris
▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10
by
Istvan Albert
96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10
by
GenoMax
125k
> there is a massive difference in performance between them. It still is taking only one minute.
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