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47
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37
replies
8.7k
views
12 follow
Forum: The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 14 months ago by 43k • written 10.7 years ago by 2.3k
110
votes
37
replies
8.4k
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 10.8 years ago by ▴ 110
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
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
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 170
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
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
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
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
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
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
244
votes
36
replies
9.7k
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
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
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
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
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
251
votes
36
replies
34k
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
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
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
59
votes
36
replies
39k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 20 months ago by ▴ 40 • written 12.0 years ago by ▴ 830
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
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
3
votes
36
replies
5.1k
views
inquiry related to snpsift
rsid snp vcf
updated 2.7 years ago by 87k • written 2.8 years ago by ▴ 140
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 7 days ago by 43k • written 5.7 years ago by ▴ 620
18
votes
36
replies
4.6k
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
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
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
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 11.1 years ago by 22k
97
votes
35
replies
26k
views
16 follow
Disease Associated Snps
snp gwas database
updated 10.3 years ago by • 0 • written 13.9 years ago by ★ 1.5k
121
votes
35
replies
43k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 11 months ago by 43k • written 6.9 years ago by ▴ 810
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
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 11 months ago by • 0 • written 8.4 years ago by ▴ 650
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
22
votes
35
replies
5.9k
views
Removing identifier with "unavailable sequence" from FASTA file
sequence genome blast RNA-Seq
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 1.9k
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
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
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 7.7 years ago by 13k
17
votes
35
replies
3.6k
views
reading blast result file
blast
7.4 years ago by nasromer2191989 ▴ 20
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
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
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
15
votes
35
replies
3.6k
views
To obtain upstream DNA sequence by giving location
SNP R genome
updated 5.4 years ago by 82k • written 5.4 years ago by ▴ 150
83
votes
34
replies
19k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 11 months ago by • 0 • written 5.8 years ago by ★ 1.3k
32
votes
34
replies
16k
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
30
votes
34
replies
6.7k
views
enrichment of gene set with enrichR
enrichR RNA-Seq R
updated 6.1 years ago by 47k • written 6.1 years ago by ▴ 30
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
1,000 results • Page 4 of 20
Recent Votes
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
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Answer: Seurat merge and batch correction
Answer: Seurat merge and batch correction
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
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Recent Replies
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by b.contreras.moreira ▴ 170
This should work if you know your sequences are related, otherwise is safer to compute local alignments with BLAST
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by yxwucq • 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error? by Mensur Dlakic ★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus by GenoMax 141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database by Art1ess • 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection by LauferVA 4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
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