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226
votes
39
replies
279k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 5 months ago by 37k • written 13.3 years ago by ▴ 620
63
votes
3
replies
263k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
expression gene Tutorial RNA-Seq protein
updated 16 months ago by 37k • written 8.7 years ago by ▴ 950
267
votes
29
replies
246k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 10 weeks ago by 37k • written 10.3 years ago by ▴ 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 37k • written 12.0 years ago by 4.8k
43
votes
24
replies
191k
views
25 follow
How To Update R In Ubuntu ?
r ubuntu
updated 10 months ago by ▴ 40 • written 9.2 years ago by ▴ 210
59
votes
12
replies
180k
views
7 follow
How To Deal With Duplicate Row Names Error In R
r
updated 13 months ago by 37k • written 10.0 years ago by ▴ 900
12
votes
6
replies
175k
views
How can I uninstall my packages in Rstudio
R Bioconductor
updated 2.4 years ago by 11k • written 5.0 years ago by ▴ 40
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 37k • written 10.9 years ago by 20k
118
votes
31
replies
170k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 16 months ago by 125k • written 12.8 years ago by 11k
124
votes
19
replies
169k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 21 months ago by • 0 • written 10.6 years ago by ▴ 350
141
votes
14
replies
162k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 3.2 years ago by ★ 2.1k • written 12.8 years ago by 152k
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 37k • written 8.4 years ago by 20k
188
votes
21
replies
161k
views
11 follow
Forward And Reverse Strand Conventions
sequence strand
updated 11 weeks ago by 96k • written 12.2 years ago by ★ 2.8k
122
votes
11
replies
155k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 17 months ago by • 0 • written 12.6 years ago by 4.8k
131
votes
18
replies
152k
views
16 follow
Blast - Formatting Output
blast format output
updated 7 weeks ago by ▴ 20 • written 9.1 years ago by ▴ 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 37k • written 10.1 years ago by ▴ 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 37k • written 10.0 years ago by ★ 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 ▴ 90 • written 9.9 years ago by 19k
10
votes
4
replies
132k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r programming
updated 11.6 years ago by 4.3k • written 11.6 years ago by ▴ 20
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 ▴ 10 • written 10.6 years ago by ▴ 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 37k • written 11.0 years ago by ★ 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 37k • written 11.9 years ago by ▴ 530
23
votes
9
replies
120k
views
8 follow
How to calculate "fold changes" in gene expression?
R gene
updated 6.5 years ago by ▴ 30 • written 7.8 years ago by ▴ 70
26
votes
10
replies
120k
views
Calculating P-Values From Z-Scores
statistics r
updated 7 months ago by 37k • written 11.0 years ago by ▴ 900
116
votes
25
replies
117k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 6.0 years ago by ▴ 160 • written 12.5 years ago by 4.8k
13
votes
8
replies
116k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 4 months ago by 37k • written 11.2 years ago by ▴ 490
160
votes
52
replies
115k
views
28 follow
Fastq Convert To Fasta
perl
9.2 years ago by biolab ★ 1.4k
3
votes
3
replies
112k
views
Find mismatch in two columns in a data frame in R
R
updated 6.9 years ago by ▴ 10 • written 6.9 years ago by ▴ 20
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 37k • written 9.8 years ago by ★ 1.5k
115
votes
21
replies
111k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 10.9 years ago by ▴ 30 • written 11.2 years ago by ★ 2.6k
97
votes
9
replies
111k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 9 months ago by ▴ 40 • written 9.4 years ago by ▴ 750
91
votes
10
replies
105k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein genes pathway analysis function
updated 10.8 years ago by ★ 2.6k • written 10.8 years ago by ★ 1.0k
28
votes
8
replies
105k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna fpkm rpkm
written 11.9 years ago by ▴ 210
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 1.5k • written 6.2 years ago by 96k
117
votes
7
replies
104k
views
Bam And Indexed Bam Files
bam index
11.1 years ago by Sahel ▴ 260
63
votes
16
replies
102k
views
11 follow
from .BAM to .BAI using samtools
sequencing samtools next-gen
updated 12 months ago by 37k • written 8.3 years ago by ▴ 860
118
votes
15
replies
101k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.1 years ago by • 0 • written 12.2 years ago by ▴ 210
31
votes
8
replies
96k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java structure algorithm
updated 12.1 years ago by • 0 • written 12.7 years ago by ▴ 70
98
votes
14
replies
95k
views
14 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 10 months ago by 7.5k • written 10.7 years ago by 12k
72
votes
25
replies
94k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 7 months ago by 37k • written 7.8 years ago by ▴ 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 ▴ 60 • written 10.7 years ago by ▴ 380
59
votes
9
replies
92k
views
10 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
RNA-Seq Blog gene expression
17 months ago by Renesh ★ 2.1k
274
votes
33
replies
90k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 12 months ago by ▴ 100 • written 9.3 years ago by 20k
173
votes
30
replies
87k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 12 months ago by 37k • written 11.8 years ago by ▴ 610
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 37k • written 13.0 years ago by 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 37k • written 8.6 years ago by ▴ 320
43
votes
15
replies
84k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna edger r counts
updated 8.2 years ago by 10k • written 11.8 years ago by ▴ 910
70
votes
16
replies
84k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 10 months ago by 152k • written 11.4 years ago by ▴ 510
39
votes
8
replies
84k
views
samtools sorting and indexing
samtools index sort
updated 3.0 years ago by ▴ 320 • written 5.6 years ago by ▴ 80
166
votes
41
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence fasta
updated 4 days ago by • 0 • written 11.6 years ago by ▴ 240
1,000 results • Page 1 of 20
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Comment: Analyzing bulk RNA-seq
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Recent Replies
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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