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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
65
votes
3
replies
281k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 6 months ago by
Ram
40k • written 9.3 years ago by
Whoknows
▴ 960
273
votes
29
replies
267k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 10 months ago by
Ram
40k • written 10.9 years ago by
sohadb1357
▴ 630
327
votes
92
replies
226k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 8 weeks ago by
kalavattam
▴ 180 • written 12.7 years ago by
Biomed
4.9k
62
votes
14
replies
189k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 5 months ago by
zx8754
11k • written 10.6 years ago by
Diana
▴ 900
282
votes
39
replies
174k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 6 months ago by
Ram
40k • written 9.1 years ago by
Obi Griffith
20k
197
votes
21
replies
171k
views
12 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 10 months ago by
Istvan Albert
98k • written 12.9 years ago by
Andrea_Bio
★ 2.8k
124
votes
13
replies
166k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 22 days ago by
Ram
40k • written 13.2 years ago by
Biomed
4.9k
135
votes
18
replies
162k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 9 months ago by
katieostrouchov
▴ 20 • written 9.8 years ago by
timjoncooper
▴ 320
93
votes
39
replies
142k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by
Dan
▴ 140 • written 11.2 years ago by
abi
▴ 380
229
votes
38
replies
140k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 3 months ago by
Ram
40k • written 10.6 years ago by
Malachi Griffith
19k
360
votes
81
replies
140k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
5 months ago by
ole.tange
★ 4.3k
146
votes
31
replies
131k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 9 weeks ago by
Ram
40k • written 11.6 years ago by
Anima Mundi
★ 2.9k
13
votes
8
replies
124k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 11 months ago by
Ram
40k • written 11.9 years ago by
Zhshqzyc
▴ 520
23
votes
9
replies
124k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 7 months ago by
Ram
40k • written 8.4 years ago by
juan.rosas1
▴ 70
762
votes
162
replies
123k
views
105 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
2.0k • written 6.8 years ago by
Istvan Albert
98k
66
votes
18
replies
116k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 3 months ago by
Ram
40k • written 9.0 years ago by
Kizuna
▴ 860
46
votes
10
replies
114k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 9 months ago by
Ram
40k • written 10.5 years ago by
biorepine
★ 1.5k
99
votes
32
replies
105k
views
21 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 7 weeks ago by
ammar.husami
• 0 • written 11.3 years ago by
GPR
▴ 390
100
votes
15
replies
104k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 6 months ago by
Genetics
▴ 20 • written 11.3 years ago by
GouthamAtla
12k
64
votes
9
replies
102k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 7 months ago by
Ram
40k • written 6.0 years ago by
Renesh
★ 2.1k
288
votes
33
replies
99k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by
Ram
40k • written 9.9 years ago by
Obi Griffith
20k
121
votes
55
replies
95k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 16 hours ago by
jl19
• 0 • written 9.3 years ago by
kay
▴ 340
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 5 days ago by
Ram
40k • written 12.3 years ago by
Palu
▴ 250
85
votes
16
replies
90k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 10 months ago by
bhanu.chandra1
▴ 50 • written 8.5 years ago by
Prakki Rama
★ 2.7k
238
votes
176
replies
88k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 4 months ago by
Ram
40k • written 8.2 years ago by
TriS
★ 4.7k
79
votes
22
replies
86k
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 months ago by
Ram
40k • written 11.9 years ago by
Hamilton
▴ 290
72
votes
20
replies
84k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 8 months ago by
Ram
40k • written 12.9 years ago by
Unode
▴ 180
97
votes
27
replies
81k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 4 months ago by
NIRJHAR
• 0 • written 11.3 years ago by
Rubal7
▴ 820
86
votes
22
replies
80k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 11 weeks ago by
sifa.khan
• 0 • written 5.2 years ago by
otwtgin2010
▴ 580
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 8 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
104
votes
12
replies
76k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 11 months ago by
Ram
40k • written 11.9 years ago by
Bioscientist
★ 1.7k
50
votes
14
replies
74k
views
10 follow
Tutorial:
Using R in Conda
R
updated 6 months ago by
Ram
40k • written 3.2 years ago by
rohitsatyam102
▴ 750
188
votes
50
replies
70k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 12 months ago by
Ram
40k • written 12.9 years ago by
Zhangleisdau
▴ 340
33
votes
17
replies
70k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 8 months ago by
Ram
40k • written 12.3 years ago by
Fahmida
▴ 80
27
votes
10
replies
70k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 6 months ago by
Ram
40k • written 2.5 years ago by
Nitin Narwade
★ 1.4k
196
votes
44
replies
69k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 8 months ago by
Ram
40k • written 11.0 years ago by
Obi Griffith
20k
40
votes
15
replies
67k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix
conversion
entrez
updated 11 months ago by
Ram
40k • written 10.2 years ago by
Josh
▴ 140
115
votes
25
replies
67k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 7 months ago by
Miguel
▴ 10 • written 12.7 years ago by
Pierre Lindenbaum
157k
75
votes
13
replies
66k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 11 months ago by
Ram
40k • written 9.9 years ago by
Nicholas Spies
★ 1.2k
56
votes
4
replies
66k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence
next-gen-sequencing
updated 11 months ago by
Ram
40k • written 8.9 years ago by
mangfu100
▴ 800
50
votes
15
replies
65k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts
sequence
fastq
updated 7 months ago by
Ram
40k • written 12.3 years ago by
Bioscientist
★ 1.7k
361
votes
58
replies
64k
views
44 follow
Forum:
Recommend Your Favorite Bioinformatics Books
books
education
written 13.6 years ago by
Istvan Albert
98k
11
votes
9
replies
64k
views
7 follow
combining fasta files
windows
fasta
notepad
updated 10 months ago by
Devarakonda
• 0 • written 8.7 years ago by
vigneshprbh37
▴ 30
92
votes
18
replies
64k
views
12 follow
Sequence length from Fasta
fasta
updated 9 months ago by
Ram
40k • written 8.9 years ago by
bongbang
▴ 80
156
votes
24
replies
60k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 3 months ago by
Ram
40k • written 10.6 years ago by
Nicolas Rosewick
10k
62
votes
22
replies
60k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf
bed
updated 9 months ago by
leshaker
• 0 • written 10.9 years ago by
biorepine
★ 1.5k
102
votes
30
replies
60k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 3 months ago by
Ram
40k • written 13.6 years ago by
Biostar User
★ 1.0k
149
votes
35
replies
60k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 7 months ago by
Ram
40k • written 10.8 years ago by
vijay
★ 1.6k
134
votes
33
replies
59k
views
19 follow
VCF files: Change Chromosome Notation
vcf
next-gen
sequence
updated 11 months ago by
Ram
40k • written 9.4 years ago by
Quak
▴ 480
1
vote
6
replies
57k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 6 months ago by
Ram
40k • written 6.7 years ago by
IOM
• 0
1,000 results • Page
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Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
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Answer: Filtering transcription factor and HOMER and ENCODE
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Answer: Have some issues in running prokka on WSL
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7.9k
It looks like the conda-installed BLAST has issues with the system's ZSTD, which is probably some WSL weirdness. You *might* be able to fix…
Comment: Network analysis with cytoscape
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Sure, the network represents the different expressed genes in my RNA-seq. I choosed string protein query.
Comment: Network analysis with cytoscape
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A few questions. 1. What does the network represent? 2. Can you insert a high level picture of the network (or pictures) if you want to zo…
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Use [deepTools' plotCorrelation function](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html).
Answer: Transcription factor co-localization p-values
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Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
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Thanks @luffy! Great material but seem they didn't mention how to customize the background genes depend on our data.
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I have calculate from this [tutorial][1]. so basically it retrieve the normalized counts matrix using `Deseq2` . Do you think it is correct…
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Let the data speak. If there's no difference, then there's no difference. Human clinical data is always messy and unpredictable, especiall…
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by
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Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation f…
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I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequenci…
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Nope, I kinda gave up. I got to the image on what fragment size is (https://www.biostars.org/p/106291/#106344) but cannot figure out how to…
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