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1,000 results • Page 1 of 20
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 37k • written 7.5 years ago by ★ 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 ▴ 50 • written 7.8 years ago by ★ 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 37k • written 11.6 years ago by ★ 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 37k • written 11.3 years ago by ▴ 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 ▴ 20 • written 10.5 years ago by ▴ 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 37k • written 12.2 years ago by ▴ 180
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 5 months ago by 37k • written 12.9 years ago by ★ 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 37k • written 7.9 years ago by ▴ 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 37k • written 10.8 years ago by ★ 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 • 0 • written 11.9 years ago by 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 ▴ 120 • written 10.7 years ago by ▴ 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 • 0 • written 8.3 years ago by ▴ 310
103
votes
12
replies
70k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 3 months ago by 37k • written 11.3 years ago by ★ 1.7k
122
votes
17
replies
69k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 10 months ago by 37k • written 11.8 years ago by ▴ 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 37k • written 11.7 years ago by ▴ 80
67
votes
18
replies
68k
views
17 follow
Project For A Beginner Bioinformatics Student
project java
updated 6 months ago by 37k • written 11.2 years ago by ▴ 230
40
votes
14
replies
68k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 9 months ago by 37k • written 12.1 years ago by ▴ 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 • 0 • written 4.5 years ago by ▴ 520
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 25 days ago by 37k • written 10.4 years ago by 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 37k • written 12.3 years ago by ▴ 340
59
votes
15
replies
66k
views
9 follow
BAM/SAM to FASTA conversion
sam bam
updated 9 months ago by 37k • written 8.0 years ago by ★ 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 37k • written 9.2 years ago by ★ 1.2k
40
votes
15
replies
64k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix conversion entrez
updated 4 months ago by 37k • written 9.6 years ago by ▴ 140
35
votes
9
replies
63k
views
8 follow
Minor allele frequency calculation
SNP next-gen
updated 8 months ago by 37k • written 8.2 years ago by ▴ 50
1,000 results • Page 1 of 20
Recent Votes
Over Representation Vs Enrichment Analysis
Answer: Using Seurat function `FindMarkers` to find differentially expressed genes betwe
C: Which genome files to use for STAR?
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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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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