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179
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I Am Preparing A Course On Ngs: Any Suggestion ?
next-gen sequencing galaxy
updated 9.1 years ago by ▴ 600 • written 11.8 years ago by 147k
32
votes
51
replies
16k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq samtools bedtools bam
updated 10.7 years ago by 24k • written 10.7 years ago by ▴ 820
26
votes
50
replies
14k
views
7 follow
Extract fasta sequences from a large file using a list of names
16s fasta extract
updated 7.3 years ago by 34k • written 7.3 years ago by ▴ 600
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
Forum
updated 8.7 years ago by ▴ 370 • written 8.7 years ago by 94k
26
votes
50
replies
9.8k
views
8 follow
Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta multi-fasta retrieval large file illumina Tool
updated 6.2 years ago by 7.4k • written 6.2 years ago by ▴ 50
12
votes
50
replies
2.4k
views
How can I find out the Linux version and what is the ftp command to install R and R Studio on Linux server?
R
5.4 years ago by thomas.f.hahn2 ▴ 100
22
votes
50
replies
14k
views
Why I can not install anything on R?
R software error
3.8 years ago by Za ▴ 140
182
votes
50
replies
64k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 11 weeks ago by 36k • written 11.8 years ago by ▴ 320
60
votes
49
replies
37k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 15 months ago by 36k • written 5.9 years ago by ★ 3.2k
72
votes
48
replies
6.2k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
tutorial education
updated 11.3 years ago by ★ 1.6k • written 11.3 years ago by 13k
39
votes
48
replies
4.7k
views
CUTADAPT in windows
sequencing
updated 7.3 years ago by 18k • written 7.3 years ago by ★ 4.1k
131
votes
48
replies
13k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 11.0 years ago by ★ 2.5k • written 11.0 years ago by 11k
72
votes
48
replies
14k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa alignment ngs tutorial Tutorial
updated 4 months ago by 36k • written 9.5 years ago by 33k
68
votes
48
replies
6.3k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2 errors Forum
updated 4.8 years ago by ★ 2.8k • written 5.1 years ago by 94k
260
votes
47
replies
19k
views
35 follow
Forum: Bioinformatics courses, workshops or training
Training Workshop Tutorial Courses Forum
4.2 years ago by Deepak Tanwar ★ 4.2k
18
votes
47
replies
3.0k
views
Fastq Trimmer by pattern
fastq trimming reads terminal
5.5 years ago by dzisis1986 ▴ 40
193
votes
47
replies
66k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 6 months ago by ▴ 10 • written 9.9 years ago by 20k
22
votes
47
replies
5.1k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 11.4 years ago by 18k • written 11.4 years ago by ★ 2.8k
22
votes
47
replies
3.3k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 3.4 years ago by ★ 2.1k • written 3.9 years ago by ▴ 460
105
votes
46
replies
11k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Forum
written 9.0 years ago by ★ 1.1k
43
votes
46
replies
2.9k
views
taking sequences of a list of miRNAs
miRNA mirbase sequence gene
updated 5.8 years ago by 36k • written 5.8 years ago by ★ 4.1k
92
votes
46
replies
9.3k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
bioinformatics programming subjective
updated 6.3 years ago by 20 • written 11.1 years ago by 3.2k
37
votes
46
replies
5.0k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code alignment programming
updated 3.9 years ago by 36k • written 12.3 years ago by 20k
123
votes
46
replies
40k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq visualization deeptools ngsplot homer Forum
updated 12 months ago by ★ 2.3k • written 6.4 years ago by ★ 3.1k
235
votes
45
replies
68k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen sequencing illumina exome human
updated 4 months ago by 36k • written 12.2 years ago by 4.8k
184
votes
45
replies
29k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
general pipeline
updated 10 months ago by 36k • written 12.5 years ago by 27k
101
votes
45
replies
77k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 4 months ago by 36k • written 10.1 years ago by ▴ 300
4
votes
45
replies
5.5k
views
SAM file wrong? help with validatesamfile
EXOME Tutorial
updated 6.0 years ago by 20 • written 6.1 years ago by ▴ 100
20
votes
45
replies
9.5k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq sequencing next-gen
updated 2.9 years ago by ▴ 10 • written 7.2 years ago by ★ 1.1k
22
votes
44
replies
10k
views
How to remove contamination from the transcriptome assembly
RNA-Seq contamination assembly blast Hiseq reads
updated 23 months ago by 20 • written 6.8 years ago by ★ 1.7k
38
votes
44
replies
21k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq next-gen alignment
updated 4.8 years ago by • 0 • written 8.3 years ago by ★ 1.4k
90
votes
44
replies
55k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 3 months ago by 36k • written 11.3 years ago by ★ 3.4k
99
votes
44
replies
20k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text r perl python
updated 4.9 years ago by ★ 2.4k • written 10.4 years ago by ★ 1.5k
126
votes
44
replies
25k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
RNA-Seq NGS adapter Forum
written 5.9 years ago by ▴ 910
151
votes
44
replies
27k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 6 weeks ago by 36k • written 8.6 years ago by ★ 2.0k
21
votes
44
replies
2.3k
views
How to analyze Illumina RNASeq data
RNA-Seq sequencing next-gen
2.0 years ago by Kumar ▴ 130
102
votes
44
replies
7.4k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
bioinformatics
updated 19 months ago by 64k • written 9.0 years ago by 24k
121
votes
44
replies
17k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
job subjective
updated 6.1 years ago by 10k • written 12.2 years ago by 5.2k
57
votes
43
replies
12k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
RNA-Seq NGS alignment genome sequence Forum
updated 18 months ago by ▴ 30 • written 3.6 years ago by 9.8k
16
votes
43
replies
4.6k
views
Stuck on calculating principal components
Vegan R software error SNP
updated 4.7 years ago by ▴ 280 • written 4.7 years ago by ★ 4.1k
19
votes
43
replies
3.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.0 years ago by nazaninhoseinkhan ▴ 430
66
votes
43
replies
24k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen sequencing parsing fastq programming
updated 6 months ago by 36k • written 11.6 years ago by ★ 2.2k
31
votes
43
replies
16k
views
11 follow
Volcano plot help code
R rna-seq
updated 4.2 years ago by ▴ 450 • written 4.3 years ago by ▴ 80
185
votes
43
replies
76k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 6 months ago by 36k • written 12.4 years ago by ★ 1.6k
151
votes
42
replies
170k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 12 weeks ago by 36k • written 10.4 years ago by 20k
56
votes
42
replies
4.7k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 6 months ago by 36k • written 7.8 years ago by 33k
28
votes
42
replies
4.7k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
5.7 years ago by mirza ▴ 170
11
votes
42
replies
2.3k
views
over presented kmer in fastq
fastqc RNA-Seq
4.8 years ago by Sam ▴ 140
8
votes
42
replies
3.2k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing program
updated 7.2 years ago by ▴ 140 • written 7.2 years ago by ▴ 290
0
votes
42
replies
1.8k
views
Database from .gbk files
database gbk ncbi
2.1 years ago by graysonford • 0
1,000 results • Page 2 of 20
Recent Votes
Why the result of GSEA and ssGSEA is different?
4-group RNAseq experiment- GSEA vs ssGSEA?
Are upset plots bad for differential expression analysis?
Answer: Are upset plots bad for differential expression analysis?
Answer: extracting sequences from a bam file
A: Best Genome Assembler and Genome Annotation tools and pipelines
Top/best RNAseq workflow including anlaysis results for function annotation
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Recent Replies
Comment: Extract sequences from a list of ID by Neel ▴ 20
Thank you....It has been done.
Comment: SNV, CNA, SV by Vincent Laufer ★ 2.2k
what exactly do you want to show about them. do you want to show the order in which they arose? or epistasis between them> ? or any other p…
Comment: Why weblogo of biopython doesn't work? by Plus • 0
Yes. I can try the web version of WebLogo, but I just want to know what kind of problem can induce to make a corrupted file by using Motif.…
Comment: Difference between clusterProfiler and gProfileR by Arup Ghosh 3.0k
> The GO terms output by gprofileR are generally quite similar to those > output by clusterProfiler, but there are small differences due to…
Comment: hgmd variants from Ensembl by Sanjar ▴ 140
Did you figure out how to do this?
Comment: Why weblogo of biopython doesn't work? by Arup Ghosh 3.0k
The `weblogo` module uses the web version of weblogo service and it seems the module is not working as intended. Instead of returning an im…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ by appropiate ▴ 40
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and…
Comment: Extract sequences from a list of ID by GenoMax 119k
You need to remove `>` from ID's as the warning tells you to do.
Comment: The best way to get gene lengths for 15K+ genes? by manaswwm ▴ 260
From my previous experiences in retrieving data in bulk from biomaRt/Ensembl - it is always better to partition your data into batches befo…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ by cmdcolin ★ 2.3k
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped …
Answer: download just a chromosome from SRA toolkit by ATpoint 64k
No, it is not possible since fastq are raw data without alignment information, hence without chromosomal information.
Answer: download just a chromosome from SRA toolkit by shelkmike ▴ 660
No, its impossible. Sequencing reads in SRA are not partitioned by chromosomes.
Comment: Extract sequences from a list of ID by Neel ▴ 20
Hi, i want to extract seq from list of id but Seqkit gives this below error and empty output file generated [WARN] symbol ">" detected…
Answer: Convert mpileup file into dataframe by ATpoint 64k
No, don't do any custom data fiddling. Follow the manual of bcftools for variant calling, it covers all you need: https://samtools.github.i…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ by GenoMax 119k
You can open multiple instances of IGV and display multiple genome alignments.
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