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1,000 results • Page 2 of 20
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32
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51
replies
17k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq samtools bedtools bam
updated 11.2 years ago by 24k • written 11.2 years ago by ▴ 820
61
votes
51
replies
20k
views
9 follow
Tool: Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
next-gen sff Tool sequence fastq
updated 14 months ago by 37k • written 8.8 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 9.5 years ago by ▴ 600 • written 12.3 years ago by 152k
12
votes
50
replies
2.7k
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
5.9 years ago by thomas.f.hahn2 ▴ 100
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
26
votes
50
replies
11k
views
8 follow
Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta multi-fasta retrieval large file illumina Tool
updated 6.6 years ago by 7.8k • written 6.7 years ago by ▴ 50
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
16s fasta extract
updated 9 hours ago by 37k • written 7.8 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 9.2 years ago by ▴ 370 • written 9.2 years ago by 96k
22
votes
50
replies
15k
views
Why I can not install anything on R?
R software error
4.3 years ago by Za ▴ 140
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 10 months ago by 37k • written 10.0 years ago by 33k
39
votes
48
replies
5.0k
views
CUTADAPT in windows
sequencing
updated 9 days ago by 37k • written 7.8 years ago by ★ 4.1k
68
votes
48
replies
6.8k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2 errors Forum
updated 5.3 years ago by ★ 2.9k • written 5.6 years ago by 96k
72
votes
48
replies
6.7k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
tutorial education
updated 11.8 years ago by ★ 1.6k • written 11.8 years ago by 13k
131
votes
48
replies
14k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 11.5 years ago by ★ 2.6k • written 11.5 years ago by 11k
261
votes
47
replies
20k
views
35 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 4 weeks ago by 37k • written 7.7 years ago by ★ 4.2k
18
votes
47
replies
3.3k
views
Fastq Trimmer by pattern
fastq trimming reads terminal
6.0 years ago by dzisis1986 ▴ 60
22
votes
47
replies
3.7k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 3.9 years ago by ★ 2.1k • written 4.3 years ago by ▴ 460
22
votes
47
replies
5.4k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 11.9 years ago by 18k • written 11.9 years ago by ★ 2.8k
124
votes
46
replies
42k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
ChIP-Seq visualization deeptools ngsplot homer Forum
updated 18 months ago by ★ 2.3k • written 6.9 years ago by ★ 3.2k
92
votes
46
replies
9.8k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
bioinformatics programming subjective
updated 6.7 years ago by 20 • written 11.6 years ago by 3.2k
43
votes
46
replies
3.1k
views
taking sequences of a list of miRNAs
miRNA mirbase sequence gene
updated 6.3 years ago by 37k • written 6.3 years ago by ★ 4.1k
105
votes
46
replies
11k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Forum
written 9.4 years ago by ★ 1.1k
37
votes
46
replies
5.3k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code alignment programming
updated 4.4 years ago by 37k • written 12.8 years ago by 21k
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
184
votes
45
replies
29k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
general pipeline
updated 16 months ago by 37k • written 12.9 years ago by 27k
4
votes
45
replies
5.9k
views
SAM file wrong? help with validatesamfile
EXOME Tutorial
updated 6.4 years ago by 20 • written 6.6 years ago by ▴ 110
20
votes
45
replies
10k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq next-gen-sequencing
updated 11 days ago by 37k • written 7.7 years ago by ★ 1.1k
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 11.6 years ago by ▴ 50 • written 12.7 years ago by 4.8k
152
votes
44
replies
28k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 7 months ago by 37k • written 9.0 years ago by ★ 2.0k
102
votes
44
replies
7.7k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
bioinformatics
updated 2.1 years ago by 68k • written 9.5 years ago by 24k
121
votes
44
replies
18k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
job subjective
updated 6.6 years ago by 11k • written 12.6 years ago by 5.3k
126
votes
44
replies
27k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
RNA-Seq NGS adapter Forum
written 6.4 years ago by ▴ 910
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 9 months ago by 37k • written 11.8 years ago by ★ 3.4k
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 5.4 years ago by ★ 2.5k • written 10.9 years ago by ★ 1.5k
22
votes
44
replies
11k
views
How to remove contamination from the transcriptome assembly
RNA-Seq contamination assembly blast Hiseq reads
updated 5 months ago by 37k • written 7.2 years ago by ★ 1.7k
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
44
votes
44
replies
22k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq next-gen alignment
updated 4 months ago by 37k • written 8.8 years ago by ★ 1.5k
21
votes
44
replies
2.7k
views
How to analyze Illumina RNASeq data
RNA-Seq sequencing next-gen
2.5 years ago by Kumar ▴ 150
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
19
votes
43
replies
3.9k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.5 years ago by nazaninhoseinkhan ▴ 490
66
votes
43
replies
25k
views
23 follow
Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
next-gen sequencing parsing fastq programming
updated 12 months ago by 37k • written 12.0 years ago by ★ 2.2k
16
votes
43
replies
5.2k
views
Stuck on calculating principal components
Vegan R software error SNP
updated 5.2 years ago by ▴ 280 • written 5.2 years ago by ★ 4.1k
31
votes
43
replies
17k
views
11 follow
Volcano plot help code
R rna-seq
updated 4.6 years ago by ▴ 450 • written 4.8 years ago by ▴ 80
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 24 months ago by ▴ 50 • written 4.0 years ago by 9.8k
122
votes
42
replies
8.6k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
biostar meta News
updated 6.1 years ago by ▴ 400 • written 10.2 years ago by 96k
11
votes
42
replies
2.8k
views
over presented kmer in fastq
fastqc RNA-Seq
5.3 years ago by Sam ▴ 150
0
votes
42
replies
2.1k
views
Database from .gbk files
database gbk ncbi
2.6 years ago by graysonford • 0
57
votes
42
replies
5.0k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 12 months ago by 37k • written 8.3 years ago by 33k
28
votes
42
replies
5.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
6.2 years ago by mirza ▴ 180
8
votes
42
replies
3.5k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 4 weeks ago by 37k • written 7.7 years ago by ▴ 290
1,000 results • Page 2 of 20
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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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