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Forum: The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 13 months ago by 43k • written 10.7 years ago by 2.3k
110
votes
37
replies
8.3k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 14 months ago by 43k • written 12.6 years ago by 161k
87
votes
37
replies
52k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 2.1 years ago by 43k • written 10.7 years ago by ▴ 110
18
votes
37
replies
13k
views
11 follow
Is it possible to download the full EpiCov database from GISAID?
GISAID genome Database EpiCoV
updated 3.0 years ago by ▴ 290 • written 4.1 years ago by ▴ 30
43
votes
37
replies
2.5k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 11 months ago by 43k • written 6.5 years ago by ★ 4.3k
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 8 days ago by • 0 • written 8.8 years ago by ▴ 170
29
votes
37
replies
3.4k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf ped phased
5.5 years ago by Shicheng Guo ★ 9.4k
130
votes
37
replies
13k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 12.6 years ago by ★ 1.3k • written 12.6 years ago by ▴ 820
5
votes
37
replies
3.5k
views
search text in one file and then replace with text from another file
search replace multiple files
6.5 years ago by mforthman ▴ 50
16
votes
37
replies
18k
views
7 follow
extracting the soft clipped seq only from a sam file
sam bam soft clip
updated 7.8 years ago by 20 • written 9.3 years ago by ★ 1.3k
36
votes
37
replies
17k
views
6 follow
How to cluster genes in heatmap
RNA-Seq R gene
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 820
17
votes
37
replies
4.7k
views
No alias or index file found for protein database
next-gen software error sequence
updated 4.9 years ago by 20 • written 5.0 years ago by ▴ 510
244
votes
36
replies
9.6k
views
32 follow
Forum: Good Habit for Bioinformatics Analyst or Scientist
Analyst Scientist
updated 12 months ago by 43k • written 8.0 years ago by ★ 9.4k
49
votes
36
replies
8.6k
views
11 follow
Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
meta biostars gsoc
updated 14 months ago by 43k • written 10.0 years ago by ▴ 110
40
votes
36
replies
14k
views
9 follow
Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score does not seem to do the trick in my case)
next-gen alignment bwa
updated 6.9 years ago by 13k • written 6.9 years ago by ▴ 130
36
votes
36
replies
37k
views
17 follow
Fetching Genbank Entries For List Of Accession Numbers.
ncbi entrez
updated 2.9 years ago by • 0 • written 11.1 years ago by ▴ 140
38
votes
36
replies
6.3k
views
11 follow
Largest Bioinformatics Software Project?
software comparison
updated 13.1 years ago by 33k • written 13.1 years ago by ▴ 40
25
votes
36
replies
13k
views
13 follow
ATAC-seq DE analysis
ATAC-seq Differential expression
updated 3.0 years ago by • 0 • written 5.9 years ago by ▴ 40
16
votes
36
replies
7.1k
views
Automating Trimmomatic for total Noobs
RNA-Seq
updated 5.2 years ago by 100k • written 5.2 years ago by ▴ 30
3
votes
36
replies
5.1k
views
inquiry related to snpsift
rsid snp vcf
updated 2.7 years ago by 87k • written 2.7 years ago by ▴ 140
18
votes
36
replies
4.5k
views
6 follow
GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip)
R
updated 17 months ago by ★ 1.9k • written 3.4 years ago by ▴ 70
84
votes
36
replies
19k
views
13 follow
Forum: Benchmark - Comparison of Different NGS Mappers
mRNA-Seq benchmark NGS-mapper
updated 2.1 years ago by 43k • written 9.3 years ago by 11k
88
votes
36
replies
40k
views
15 follow
1000 Genomes Ld Calculation
genome linkage gwas
updated 10.2 years ago by ▴ 970 • written 13.5 years ago by ★ 3.4k
10
votes
36
replies
5.7k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 2 days ago by 43k • written 5.7 years ago by ▴ 620
251
votes
36
replies
33k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 13 months ago by 43k • written 14.0 years ago by 161k
59
votes
36
replies
39k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 20 months ago by ▴ 40 • written 11.9 years ago by ▴ 830
11
votes
36
replies
34k
views
6 follow
python script error: ImportError: No module named pysam
pysam pythonscript .py overlapsignature
updated 5.9 years ago by ★ 2.1k • written 5.9 years ago by ▴ 110
34
votes
35
replies
17k
views
8 follow
Sample names for TCGA data from GDC-legacy archive
RNA-Seq tcga gdc
updated 5.1 years ago by ▴ 30 • written 6.1 years ago by ▴ 770
149
votes
35
replies
62k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 14 months ago by 43k • written 11.4 years ago by ★ 1.6k
15
votes
35
replies
3.6k
views
To obtain upstream DNA sequence by giving location
SNP R genome
updated 5.4 years ago by 81k • written 5.4 years ago by ▴ 150
65
votes
35
replies
20k
views
17 follow
Which Dna Compression Algorithms Are Actually Used?
dna
updated 20 months ago by 161k • written 12.9 years ago by ▴ 270
97
votes
35
replies
26k
views
16 follow
Disease Associated Snps
snp gwas database
updated 10.2 years ago by • 0 • written 13.9 years ago by ★ 1.5k
5
votes
35
replies
3.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome vg
updated 9 months ago by ▴ 460 • written 10 months ago by • 0
116
votes
35
replies
8.2k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 14 months ago by 43k • written 11.0 years ago by 22k
17
votes
35
replies
3.6k
views
reading blast result file
blast
7.4 years ago by nasromer2191989 ▴ 20
22
votes
35
replies
5.9k
views
Removing identifier with "unavailable sequence" from FASTA file
sequence genome blast RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ★ 1.9k
14
votes
35
replies
10k
views
8 follow
Converting large (compressed and unsorted) BAM files to fastq
BAM fatsq alignment bedtools picard
updated 2.7 years ago by 141k • written 7.4 years ago by ▴ 580
40
votes
35
replies
13k
views
10 follow
find positions of a short sequence in a genome
sequence search
updated 8 months ago by ★ 1.5k • written 7.6 years ago by 13k
57
votes
35
replies
14k
views
9 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP genotype GATK
updated 6 months ago by 87k • written 6.2 years ago by ▴ 520
79
votes
35
replies
9.6k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 10 months ago by • 0 • written 8.4 years ago by ▴ 650
45
votes
35
replies
6.1k
views
12 follow
Forum: looking for a bioinformatics project to do during military rotation
military
updated 22 months ago by 43k • written 6.6 years ago by ▴ 60
26
votes
35
replies
32k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 14 months ago by ▴ 10 • written 10.1 years ago by ★ 4.1k
121
votes
35
replies
43k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 11 months ago by 43k • written 6.8 years ago by ▴ 810
4
votes
35
replies
9.6k
views
Is They Any Software Or Technique To Find The Number Of Reads Mapped To Each Contig After Aligment
mapping RNA-seq
updated 13 months ago by 43k • written 10.3 years ago by ▴ 50
2
votes
35
replies
11k
views
BWA-MEM using long PacBio reads
PacBio alignement bwa-mem sam
updated 7.3 years ago by 20k • written 7.3 years ago by ★ 1.4k
83
votes
34
replies
19k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 10 months ago by • 0 • written 5.8 years ago by ★ 1.3k
32
votes
34
replies
15k
views
10 follow
How To Randomly Sample A Subset Of Lines From A Bed File
bed chip-seq
updated 2.5 years ago by 43k • written 10.5 years ago by ▴ 540
36
votes
34
replies
2.8k
views
9 follow
Forum: New to bioinformatics.....
gene
updated 11 months ago by 43k • written 6.1 years ago by • 0
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq demultiplexing
updated 6 weeks ago by ★ 2.1k • written 6.7 years ago by ▴ 350
103
votes
34
replies
113k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 3 months ago by 43k • written 11.9 years ago by ▴ 390
1,000 results • Page 4 of 20
Recent Votes
Bedtools merge but only if intersection exists
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: Korean human genome reference file by SeoGyun • 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool by Ashok • 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo) by cmdcolin ★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB by 航太郎 • 0
Thanks for your guide!
Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org by Ram 43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you so much
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you very much
Answer: Downloaded pdb's on rcsb.org by Ram 43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool by GenoMax 141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
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