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106,525 results • Page 2 of 2131
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61
votes
51
replies
20k
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9 follow
Tool: Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
next-gen sff Tool sequence fastq
updated 12 months ago by 37k • written 8.6 years ago by ▴ 790
179
votes
51
replies
15k
views
26 follow
I Am Preparing A Course On Ngs: Any Suggestion ?
next-gen sequencing galaxy
updated 9.4 years ago by ▴ 600 • written 12.1 years ago by 150k
26
votes
50
replies
10k
views
8 follow
Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta multi-fasta retrieval large file illumina Tool
updated 6.5 years ago by 7.7k • written 6.5 years ago by ▴ 50
182
votes
50
replies
66k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 8 weeks ago by 37k • written 12.1 years ago by ▴ 320
12
votes
50
replies
2.6k
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
5.7 years ago by thomas.f.hahn2 ▴ 100
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 9.0 years ago by ▴ 370 • written 9.0 years ago by 95k
26
votes
50
replies
14k
views
7 follow
Extract fasta sequences from a large file using a list of names
16s fasta extract
updated 7.6 years ago by 34k • written 7.6 years ago by ▴ 600
22
votes
50
replies
14k
views
Why I can not install anything on R?
R software error
4.1 years ago by Za ▴ 140
60
votes
49
replies
37k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 18 months ago by 37k • written 6.2 years ago by ★ 3.3k
39
votes
48
replies
4.9k
views
CUTADAPT in windows
sequencing
updated 7.6 years ago by 18k • written 7.6 years ago by ★ 4.1k
131
votes
48
replies
13k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 11.3 years ago by ★ 2.6k • written 11.3 years ago by 11k
72
votes
48
replies
6.4k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
tutorial education
updated 11.6 years ago by ★ 1.6k • written 11.6 years ago by 13k
68
votes
48
replies
6.6k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2 errors Forum
updated 5.1 years ago by ★ 2.9k • written 5.4 years ago by 95k
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa alignment ngs tutorial Tutorial
updated 7 months ago by 37k • written 9.8 years ago by 33k
261
votes
47
replies
20k
views
35 follow
Forum: Bioinformatics courses, workshops or training
Training Workshop Tutorial Courses Forum
updated 25 days ago by 37k • written 7.5 years ago by ★ 4.2k
22
votes
47
replies
3.5k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 3.7 years ago by ★ 2.1k • written 4.2 years ago by ▴ 460
18
votes
47
replies
3.2k
views
Fastq Trimmer by pattern
fastq trimming reads terminal
5.8 years ago by dzisis1986 ▴ 60
22
votes
47
replies
5.2k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 11.7 years ago by 18k • written 11.7 years ago by ★ 2.8k
124
votes
46
replies
41k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq visualization deeptools ngsplot homer Forum
updated 16 months ago by ★ 2.3k • written 6.7 years ago by ★ 3.2k
37
votes
46
replies
5.2k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code alignment programming
updated 4.2 years ago by 37k • written 12.6 years ago by 21k
43
votes
46
replies
2.9k
views
taking sequences of a list of miRNAs
miRNA mirbase sequence gene
updated 6.1 years ago by 37k • written 6.1 years ago by ★ 4.1k
92
votes
46
replies
9.6k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
bioinformatics programming subjective
updated 6.5 years ago by 20 • written 11.4 years ago by 3.2k
105
votes
46
replies
11k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Forum
written 9.3 years ago by ★ 1.1k
4
votes
45
replies
5.8k
views
SAM file wrong? help with validatesamfile
EXOME Tutorial
updated 6.3 years ago by 20 • written 6.4 years ago by ▴ 110
20
votes
45
replies
9.9k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq sequencing next-gen
updated 11 weeks ago by 37k • written 7.5 years ago by ★ 1.1k
184
votes
45
replies
29k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
general pipeline
updated 14 months ago by 37k • written 12.8 years ago by 27k
235
votes
45
replies
69k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen sequencing illumina exome human
updated 11.5 years ago by ▴ 50 • written 12.5 years ago by 4.8k
105
votes
45
replies
78k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 12 weeks ago by ▴ 10 • written 10.4 years ago by ▴ 320
43
votes
44
replies
21k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq next-gen alignment
updated 9 weeks ago by 37k • written 8.6 years ago by ★ 1.5k
102
votes
44
replies
7.6k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
bioinformatics
updated 23 months ago by 66k • written 9.3 years ago by 24k
90
votes
44
replies
56k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 7 months ago by 37k • written 11.6 years ago by ★ 3.4k
121
votes
44
replies
18k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
job subjective
updated 6.4 years ago by 11k • written 12.4 years ago by 5.3k
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 6 weeks ago by 37k • written 10.2 years ago by 20k
21
votes
44
replies
2.6k
views
How to analyze Illumina RNASeq data
RNA-Seq sequencing next-gen
2.3 years ago by Kumar ▴ 140
151
votes
44
replies
27k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 5 months ago by 37k • written 8.9 years ago by ★ 2.0k
22
votes
44
replies
11k
views
How to remove contamination from the transcriptome assembly
RNA-Seq contamination assembly blast Hiseq reads
updated 3 months ago by 37k • written 7.1 years ago by ★ 1.7k
99
votes
44
replies
21k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text r perl python
updated 5.2 years ago by ★ 2.5k • written 10.7 years ago by ★ 1.5k
126
votes
44
replies
26k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
RNA-Seq NGS adapter Forum
written 6.2 years ago by ▴ 910
16
votes
43
replies
5.0k
views
Stuck on calculating principal components
Vegan R software error SNP
updated 5.0 years ago by ▴ 280 • written 5.0 years ago by ★ 4.1k
19
votes
43
replies
3.7k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.3 years ago by nazaninhoseinkhan ▴ 480
31
votes
43
replies
16k
views
11 follow
Volcano plot help code
R rna-seq
updated 4.4 years ago by ▴ 450 • written 4.6 years ago by ▴ 80
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 10 months ago by 37k • written 11.9 years ago by ★ 2.2k
185
votes
43
replies
77k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 11 weeks ago by 37k • written 12.7 years ago by ★ 1.6k
57
votes
43
replies
13k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
RNA-Seq NGS alignment genome sequence Forum
updated 21 months ago by ▴ 50 • written 3.9 years ago by 9.8k
57
votes
42
replies
4.9k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 10 months ago by 37k • written 8.1 years ago by 33k
122
votes
42
replies
8.5k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
biostar meta News
updated 5.9 years ago by ▴ 380 • written 10.0 years ago by 95k
28
votes
42
replies
5.0k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
6.0 years ago by mirza ▴ 180
11
votes
42
replies
2.5k
views
over presented kmer in fastq
fastqc RNA-Seq
5.1 years ago by Sam ▴ 150
8
votes
42
replies
3.4k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing program
updated 7.5 years ago by ▴ 140 • written 7.5 years ago by ▴ 290
151
votes
42
replies
172k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 6 months ago by 37k • written 10.7 years ago by 20k
106,525 results • Page 2 of 2131
Recent Votes
Comment: How to dealign MSAs? Or how best to merge MSAs?
A: DESeq2 - "all gene-wise dispersion estimates are within 2 orders of magnitude"
C: DESeq2 - "all gene-wise dispersion estimates are within 2 orders of magnitude"
Answer: Extracting Novel SNPs from VEP output
Comment: extracting chip id for a transcription factor
Answer: Require suggestion for python tools that can implement VCF file into FASTA files
FigTree and ggtree
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Recent Replies
Comment: How to dealign MSAs? Or how best to merge MSAs? by GenoMax 123k
You will have to explain 10x10 MSA (I am not familiar with that term)? You don't have the aligned data in a standard MSA alignment format (…
Comment: Bedtools merge but only if intersection exists by jonathan.rosenski ▴ 10
Actually my bedtools v2.27.1 returns a 3 column bed file with -wa -wb
Comment: How to dealign MSAs? Or how best to merge MSAs? by jbt38 • 0
Thanks, but what do you mean? I do not have access to the pre-aligned fastas, only the 10x10 MSAs. What I would like to do is just dealig…
Answer: Bedtools merge but only if intersection exists by jonathan.rosenski ▴ 10
Thank you all
Answer: How to work with long read (Pacbio) Data from SRA by GenoMax 123k
If you look at this project in [**SRA Run Selector**][1] (I have sorted the table so you see PacBio data at top) you can see that there wer…
Comment: Bedtools merge but only if intersection exists by ATpoint 66k
requires some awk, see below
Answer: Bedtools merge but only if intersection exists by ATpoint 66k
Assuming a three-column BED file you could do this, with an awk command as `-wa -wb` will make a 6-column BED file after the intersect: ``…
Comment: Analysis of Nanopore cDNA sequencing data by GenoMax 123k
Using the top level assembly should be fine. > then align them to the same genome using minimap2 after filtering for > quality >8 Not sur…
Comment: Star indexing by ATpoint 66k
I would also apply the suggestion in the warning if I was you and generally remove all whitespaces and non-standard characters from file na…
Comment: Bedtools merge but only if intersection exists by jonathan.rosenski ▴ 10
ah ok. I did not know you could do -wa -wb. Thanks
Comment: Bedtools merge but only if intersection exists by ATpoint 66k
It's as you say just a pipe of two commands, I do not see the downside of that: <s>bedtools intersect -a first.bed -b second.bed -wa -wb |…
Comment: Locating IBD candidates with just VCF files by 4galaxy77 2.5k
Did you use a reference panel? If you didn't then yes trying to phase 11 individuals without one is going to give you pretty rubbish result…
Comment: Is it possible to run CibersortX with a very small number of samples? by ummscr • 0
Hi - Did you solve this issue, I am having the same problem
Comment: warning when installing "AnnotationDbi" by bkleiboeker ▴ 50
Are you using BiocManager::install()?
Comment: Need help in microarray data analysis by seidel 9.8k
What was the solution?
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