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226
votes
39
replies
277k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 7 weeks ago by 37k • written 12.9 years ago by ▴ 620
58
votes
3
replies
251k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
expression gene Tutorial RNA-Seq protein
updated 11 months ago by 37k • written 8.3 years ago by ▴ 920
263
votes
29
replies
234k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 1 day ago by • 0 • written 9.9 years ago by ▴ 610
315
votes
90
replies
202k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 6 days ago by 37k • written 11.7 years ago by 4.8k
43
votes
24
replies
187k
views
25 follow
How To Update R In Ubuntu ?
r ubuntu
updated 5 months ago by ▴ 30 • written 8.8 years ago by ▴ 210
59
votes
12
replies
175k
views
7 follow
How To Deal With Duplicate Row Names Error In R
r
updated 9 months ago by 37k • written 9.6 years ago by ▴ 900
151
votes
42
replies
171k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 4 months ago by 37k • written 10.6 years ago by 20k
12
votes
6
replies
167k
views
How can I uninstall my packages in Rstudio
R Bioconductor
updated 2.1 years ago by 11k • written 4.7 years ago by ▴ 40
120
votes
19
replies
166k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 17 months ago by • 0 • written 10.3 years ago by ▴ 340
138
votes
14
replies
160k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 2.9 years ago by ★ 2.1k • written 12.5 years ago by 149k
118
votes
31
replies
158k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 12 months ago by 120k • written 12.5 years ago by 11k
183
votes
19
replies
156k
views
9 follow
Forward And Reverse Strand Conventions
sequence strand
updated 11.7 years ago by 49k • written 11.9 years ago by ★ 2.8k
271
votes
39
replies
155k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 5 months ago by 37k • written 8.1 years ago by 20k
121
votes
11
replies
150k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 13 months ago by • 0 • written 12.2 years ago by 4.8k
126
votes
19
replies
147k
views
14 follow
Blast - Formatting Output
blast format output
updated 2.0 years ago by • 0 • written 8.8 years ago by ▴ 300
147
votes
8
replies
136k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 11 weeks ago by 37k • written 9.8 years ago by ▴ 400
356
votes
80
replies
133k
views
32 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
next-gen parallel ngs Tool tools
updated 6 months ago by 37k • written 9.6 years ago by ★ 4.3k
10
votes
4
replies
130k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r programming
updated 11.2 years ago by 4.3k • written 11.2 years ago by ▴ 20
220
votes
37
replies
129k
views
28 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 1 day ago by 37k • written 9.6 years ago by 19k
139
votes
30
replies
119k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line command-line fasta list bash
updated 16 days ago by 37k • written 10.6 years ago by ★ 2.9k
26
votes
10
replies
119k
views
Calculating P-Values From Z-Scores
statistics r
updated 3 months ago by 37k • written 10.6 years ago by ▴ 900
129
votes
32
replies
119k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 5 months ago by 37k • written 11.6 years ago by ▴ 530
23
votes
9
replies
118k
views
8 follow
How to calculate "fold changes" in gene expression?
R gene
updated 6.1 years ago by ▴ 30 • written 7.4 years ago by ▴ 70
85
votes
38
replies
116k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 21 days ago by • 0 • written 10.2 years ago by ▴ 370
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 5.6 years ago by ▴ 160 • written 12.2 years ago by 4.8k
13
votes
8
replies
111k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 11 weeks ago by 37k • written 10.9 years ago by ▴ 490
158
votes
52
replies
111k
views
28 follow
Fastq Convert To Fasta
perl
8.9 years ago by biolab ★ 1.4k
115
votes
21
replies
110k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 10.5 years ago by ▴ 30 • written 10.9 years ago by ★ 2.6k
3
votes
3
replies
110k
views
Find mismatch in two columns in a data frame in R
R
updated 6.6 years ago by ▴ 10 • written 6.6 years ago by ▴ 20
46
votes
10
replies
109k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm rpkm rna-seq
updated 2.8 years ago by ★ 2.1k • written 9.5 years ago by ★ 1.5k
97
votes
10
replies
106k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 5 months ago by ▴ 30 • written 9.0 years ago by ▴ 750
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 10.5 years ago by ★ 2.5k • written 10.5 years ago by ★ 1.0k
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 11.5 years ago by ▴ 210
115
votes
7
replies
100k
views
Bam And Indexed Bam Files
bam index
10.7 years ago by Sahel ▴ 240
118
votes
15
replies
100k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 11.7 years ago by • 0 • written 11.9 years ago by ▴ 210
695
votes
159
replies
96k
views
99 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training tutorial News handbook
updated 14 days ago by 1.1k • written 5.8 years ago by 94k
31
votes
8
replies
95k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java structure algorithm
updated 11.7 years ago by • 0 • written 12.4 years ago by ▴ 70
61
votes
16
replies
95k
views
11 follow
from .BAM to .BAI using samtools
sequencing samtools next-gen
updated 8 months ago by 37k • written 8.0 years ago by ▴ 860
93
votes
14
replies
90k
views
14 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 6 months ago by 7.2k • written 10.3 years ago by 12k
88
votes
31
replies
88k
views
20 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 7 months ago by ▴ 60 • written 10.3 years ago by ▴ 380
59
votes
9
replies
88k
views
8 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
RNA-Seq Blog gene expression
13 months ago by Renesh ★ 2.1k
71
votes
25
replies
86k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 3 months ago by 37k • written 7.4 years ago by ▴ 230
172
votes
30
replies
86k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 8 months ago by 37k • written 11.5 years ago by ▴ 600
270
votes
33
replies
86k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 8 months ago by ▴ 100 • written 8.9 years ago by 20k
95
votes
19
replies
84k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 7 weeks ago by 37k • written 12.6 years ago by 27k
43
votes
15
replies
83k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna edger r counts
updated 7.9 years ago by 9.6k • written 11.5 years ago by ▴ 910
69
votes
16
replies
81k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 6 months ago by 149k • written 11.0 years ago by ▴ 510
114
votes
52
replies
81k
views
21 follow
How to plot coverage and depth statistics of a bam file
sequencing coverage bam depth next-gen
updated 9 weeks ago by • 0 • written 8.3 years ago by ▴ 320
234
votes
176
replies
80k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 18 months ago by 37k • written 7.2 years ago by ★ 4.6k
37
votes
8
replies
80k
views
samtools sorting and indexing
samtools index sort
updated 2.7 years ago by ▴ 310 • written 5.2 years ago by ▴ 80
1,000 results • Page 1 of 20
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Answer: "RNA-seq by Example" Differential Gene Expression Error
Answer: "RNA-seq by Example" Differential Gene Expression Error
Answer: Microarray DEG analysis visualisation
C: differential expression analysis with DESeq2 & edgeR
Answer: Are alternative splicing analysis and differential expression analysis of RNA-se
differential expression analysis with DESeq2 & edgeR
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Recent Replies
Comment: Convert Gene Ensemble IDs to Gene Symbols on R by igor 13k
Novel genes used to be assigned temporary cryptic placeholder symbols like AC010680.1 or LINC02050 or C1orf43. They recently stopped doing …
Answer: "RNA-seq by Example" Differential Gene Expression Error by Jeremy ▴ 590
Got it. I missed that update. Thanks a lot!
Comment: My ensembl requests are suddenly very slow - why? by GenoMax 120k
Perhaps there is an error in the compara database for that entry. Can you remove that and see if your job proceeds?
Comment: My ensembl requests are suddenly very slow - why? by ngarber ▴ 50
It shows as error 503: "service unavailable" when I click that link... also, here's a strange thing, I just tried from another internet con…
Answer: Kraken 2 example txt files by Istvan Albert 94k
There is a new paper out on Kraken 2, they ought to have some results: * Metagenome analysis using the Kraken software suite https://…
Comment: My ensembl requests are suddenly very slow - why? by GenoMax 120k
That ID does have homologs available: https://usa.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000185104;r=1:50437028-509…
Answer: "RNA-seq by Example" Differential Gene Expression Error by GenoMax 120k
You create the `design.csv` file using an editor in step 3 of the step-by-step process. It needs to contain the following: sample,co…
Comment: Dramatic decrease of mapping efficiency between Bwameth and Bismark by reza.jabal ▴ 560
What model organism are you using in your experiment? Human, model organism or non-model organism?
Comment: Ensembl Homology REST requests - possible to download whole database and query l by ngarber ▴ 50
So for looking at homologs of human proteins, do I want the following file? http://ftp.ensembl.org/pub/current_compara/conservation_sc…
Comment: My ensembl requests are suddenly very slow - why? by ngarber ▴ 50
The requests.get() method is giving me the status code 200 (OK) when I invoke response.status_code and slowly iterates over my list of IDs …
Answer: My ensembl requests are suddenly very slow - why? by GenoMax 120k
This question is probably not easily answerable. It is possible that Ensembl server is simply overloaded at the moment and you are feeling …
Comment: CNVKIT import errors by GenoMax 120k
Please use `conda` to do the installation. A basic tutorial is available here to use `conda` (use the part for `conda`): https://www.biosta…
Comment: CNVKIT import errors by ptoru001 • 0
hi all i am having similar errors with installation of cnvkit (for mac)...and cannot seem to figure it out...would anyone kindly please hel…
Comment: Ensembl Homology REST requests - possible to download whole database and query l by Pierre Lindenbaum 149k
>possible to download whole database and query locally? http://ftp.ensembl.org/pub/current_compara/
Comment: High number of unmapped reads in STAR by Negara • 0
I have added a link in my original post to the genome files I am using. These are human samples (paired end reads). I wonder why this much …
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