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1,000 results • Page 3 of 20
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8
votes
42
replies
4.1k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 9 months ago by 40k • written 8.3 years ago by ▴ 290
11
votes
42
replies
3.4k
views
over presented kmer in fastq
fastqc RNA-Seq
6.0 years ago by Sam ▴ 150
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
151
votes
42
replies
177k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 16 months ago by 40k • written 11.6 years ago by 20k
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
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
5
votes
41
replies
2.3k
views
Insert sequence in nt database
nt
3.4 years ago by anasofiamoreira94 ▴ 80
23
votes
41
replies
3.2k
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
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
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
92k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 8 days ago by 40k • written 12.3 years ago by ▴ 250
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
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
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
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
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
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 7.3 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
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
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
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 12.0 years ago by ▴ 310 • written 12.0 years ago by ★ 1.3k
10
votes
40
replies
5.7k
views
weird insert size post trimming
RNA-Seq
updated 6.1 years ago by ★ 2.9k • written 6.1 years ago by ▴ 280
151
votes
39
replies
24k
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
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
11
votes
39
replies
3.4k
views
Any advice for a de novo genome assembly
k-mer de novo genome assembly
updated 6.9 years ago by ▴ 60 • written 6.9 years ago by ▴ 640
25
votes
39
replies
5.0k
views
8 follow
Forum: Bioinformatics Study Group
study-group
updated 7 months ago by 40k • written 10.3 years ago by ▴ 440
226
votes
39
replies
285k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 13 months ago by 40k • written 13.9 years ago by ▴ 620
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
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
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
55
votes
39
replies
5.1k
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
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
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 13.6 years ago by ▴ 310
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
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
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 2 days ago by 21k • written 9.9 years ago by ★ 3.6k
48
votes
38
replies
16k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 5 months ago by 40k • written 7.6 years ago by 11k
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
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
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
129
votes
38
replies
6.7k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 4 months ago by 40k • written 4.5 years ago by 98k
53
votes
38
replies
3.9k
views
10 follow
Multiple alignment software
alignment clustal omega tcoffee
updated 4.0 years ago by 98k • written 4.0 years ago by ▴ 130
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
16
votes
37
replies
16k
views
7 follow
extracting the soft clipped seq only from a sam file
sam bam soft clip
updated 7.2 years ago by 20 • written 8.7 years ago by ★ 1.3k
130
votes
37
replies
12k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 12.1 years ago by ★ 1.3k • written 12.1 years ago by ▴ 820
1,000 results • Page 3 of 20
Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Recent Replies
Comment: bedtools intersect by position & stand not working even with common regions by rfran010 ▴ 830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files by rfran010 ▴ 830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly. If it's not done alre…
Answer: vcf.gz to vcf by Mark ★ 1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names? by Jiyao Wang ▴ 340
You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow? by Mark ★ 1.3k
Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'. Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files by GenoMax 134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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