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1,000 results • Page 3 of 20
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11
votes
42
replies
3.4k
views
over presented kmer in fastq
fastqc RNA-Seq
6.0 years ago by Sam ▴ 150
28
votes
42
replies
6.2k
views
7 follow
How to add tophat and bowtie to the path?
export PATH bowtie2.2.9 tophat2
6.8 years ago by mirza ▴ 180
122
votes
42
replies
9.4k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 7 months ago by 40k • written 10.8 years ago by 98k
8
votes
42
replies
4.1k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 8 months ago by 40k • written 8.3 years ago by ▴ 290
138
votes
42
replies
21k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 6 months ago by 3.7k • written 10.3 years ago by ★ 1.6k
57
votes
42
replies
5.8k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 20 months ago by 40k • written 9.0 years ago by 33k
5
votes
41
replies
2.3k
views
Insert sequence in nt database
nt
3.4 years ago by anasofiamoreira94 ▴ 80
19
votes
41
replies
8.0k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by ▴ 80
31
votes
41
replies
2.0k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 3 months ago by 40k • written 3.6 years ago by ▴ 40
18
votes
41
replies
12k
views
6 follow
paired end illumina reads
Assembly paired end
updated 14 months ago by 40k • written 7.9 years ago by ▴ 290
23
votes
41
replies
3.1k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS biopython illumina WGS
updated 4 months ago by 40k • written 5 months ago by ▴ 30
98
votes
41
replies
5.1k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error next-gen-sequencing
updated 5 months ago by 40k • written 7.1 years ago by ▴ 510
13
votes
41
replies
1.9k
views
Is my file created completely
sam BWA-MEM BWA
updated 6 months ago by 40k • written 6.4 years ago by ▴ 10
16
votes
41
replies
8.4k
views
How to extract information from headers of fasta file
sequence
updated 15 months ago by 40k • written 8.5 years ago by ▴ 70
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 4 days ago by 40k • written 12.3 years ago by ▴ 250
203
votes
41
replies
24k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 7 months ago by 40k • written 8.9 years ago by ★ 5.2k
38
votes
41
replies
54k
views
9 follow
Volcano Plot from DEseq2
R
written 5.9 years ago by ★ 1.1k
26
votes
41
replies
15k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 10 months ago by • 0 • written 5.7 years ago by ▴ 120
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.2 years ago by ▴ 170
6
votes
40
replies
9.8k
views
Fastx_Collapser Has No Fastq Output
fastx RNA-seq
updated 7 months ago by 40k • written 10.0 years ago by ▴ 240
10
votes
40
replies
5.6k
views
weird insert size post trimming
RNA-Seq
updated 6.1 years ago by ★ 2.9k • written 6.1 years ago by ▴ 280
68
votes
40
replies
5.4k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen sequencing sequencing
updated 11.9 years ago by ▴ 310 • written 11.9 years ago by ★ 1.3k
40
votes
40
replies
10k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq alignment
updated 5.6 years ago by 86k • written 7.0 years ago by ▴ 550
67
votes
40
replies
8.7k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 19 months ago by 40k • written 8.9 years ago by ★ 2.9k
16
votes
40
replies
5.4k
views
About TCGA CNV data preprocessing
SNP CNV
updated 5.0 years ago by 86k • written 5.0 years ago by ▴ 40
151
votes
39
replies
23k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 7 months ago by 40k • written 10.7 years ago by 3.0k
20
votes
39
replies
8.6k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast blast memory
updated 8.0 years ago by ▴ 170 • written 11.7 years ago by ▴ 160
25
votes
39
replies
5.0k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 7 months ago by 40k • written 10.2 years ago by ▴ 440
55
votes
39
replies
5.0k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf python perl awk
updated 11.1 years ago by 8.2k • written 11.1 years ago by ▴ 310
69
votes
39
replies
3.8k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 4 months ago by 40k • written 6.3 years ago by 13k
11
votes
39
replies
3.4k
views
Any advice for a de novo genome assembly
k-mer de novo genome assembly
updated 6.8 years ago by ▴ 60 • written 6.9 years ago by ▴ 640
66
votes
39
replies
6.9k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career subjective
updated 2.5 years ago by 40k • written 13.5 years ago by ▴ 310
81
votes
39
replies
6.6k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 7 months ago by 40k • written 10.7 years ago by 98k
93
votes
39
replies
142k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by ▴ 140 • written 11.2 years ago by ▴ 380
36
votes
39
replies
3.2k
views
11 follow
Forum: Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast RNA-Seq alignment next-gen-sequencing
updated 4 months ago by 40k • written 5.9 years ago by ▴ 130
282
votes
39
replies
174k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
18
votes
39
replies
3.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 4 months ago by 40k • written 4.5 years ago by ▴ 50
226
votes
39
replies
284k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 13 months ago by 40k • written 13.9 years ago by ▴ 620
27
votes
38
replies
19k
views
Heatmap based with FPKM values
RNA-Seq next-gen R
updated 4.4 years ago by 20 • written 5.9 years ago by ▴ 820
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 27 days ago by 21k • written 9.9 years ago by ★ 3.6k
129
votes
38
replies
6.7k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 3 months ago by 40k • written 4.5 years ago by 98k
229
votes
38
replies
140k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 3 months ago by 40k • written 10.6 years ago by 19k
53
votes
38
replies
3.8k
views
10 follow
Multiple alignment software
alignment clustal omega tcoffee
updated 4.0 years ago by 98k • written 4.0 years ago by ▴ 130
39
votes
38
replies
7.7k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 13 months ago by 40k • written 7.9 years ago by 13k
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 17 months ago by 40k • written 8.6 years ago by ▴ 920
48
votes
38
replies
16k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 5 months ago by 40k • written 7.5 years ago by 11k
47
votes
37
replies
7.9k
views
12 follow
Forum: The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 7 months ago by 40k • written 10.1 years ago by 2.3k
29
votes
37
replies
2.9k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf ped phased
4.9 years ago by Shicheng Guo ★ 9.3k
43
votes
37
replies
1.9k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 4 months ago by 40k • written 6.0 years ago by ★ 4.2k
87
votes
37
replies
49k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 18 months ago by 40k • written 10.2 years ago by ▴ 110
1,000 results • Page 3 of 20
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Popular Question to bharata1803 ▴ 550
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Recent Replies
Answer: Fetch Fastq files directly for SRA data by Rob 6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe by YUYANG.OON • 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject by Qi • 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis? by Yogi ▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions by Yogi ▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question by Istvan Albert 98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate by dsull ★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes? by Michael 53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate by Mehwish • 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting by Ram 40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting by bk11 ★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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