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21,408 results • Page 2 of 429
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Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 10 months ago by 37k • written 8.2 years ago by ★ 5.1k
67
votes
40
replies
8.0k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 11 months ago by 37k • written 8.2 years ago by ★ 2.9k
273
votes
39
replies
162k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 9 months ago by 37k • written 8.4 years ago by 20k
226
votes
39
replies
280k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 5 months ago by 37k • written 13.3 years ago by ▴ 620
39
votes
38
replies
6.9k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 5 months ago by 37k • written 7.2 years ago by 13k
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 9 months ago by 37k • written 8.0 years ago by ▴ 920
159
votes
38
replies
15k
views
22 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
bioinformatics Forum humor
updated 4 months ago by ▴ 30 • written 9.9 years ago by 96k
220
votes
38
replies
132k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 7 weeks ago by ▴ 90 • written 9.9 years ago by 19k
89
votes
38
replies
124k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by ▴ 10 • written 10.6 years ago by ▴ 370
87
votes
37
replies
47k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 11 months ago by 37k • written 9.5 years ago by ▴ 110
49
votes
36
replies
7.1k
views
11 follow
Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
gsoc meta biostar feature bug
updated 4 months ago by 37k • written 8.8 years ago by ▴ 110
9
votes
36
replies
2.4k
views
6 follow
GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip)
R
updated 12 weeks ago by ★ 1.7k • written 2.2 years ago by ▴ 30
99
votes
36
replies
27k
views
32 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 13 days ago by 21k • written 9.2 years ago by ★ 3.6k
8
votes
36
replies
9.7k
views
18 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 9 weeks ago by 37k • written 7.6 years ago by ▴ 160
251
votes
36
replies
30k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
file
updated 4 months ago by 84k • written 12.8 years ago by 152k
84
votes
36
replies
16k
views
13 follow
Forum: Benchmark - Comparison of Different NGS Mappers
mRNA-Seq benchmark NGS-mapper
updated 10 months ago by 37k • written 8.1 years ago by 9.8k
59
votes
36
replies
33k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 6 months ago by ▴ 40 • written 10.7 years ago by ▴ 820
146
votes
35
replies
57k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 9 months ago by • 0 • written 10.2 years ago by ★ 1.6k
22
votes
35
replies
4.5k
views
Removing identifier with "unavailable sequence" from FASTA file
sequence genome blast RNA-Seq
updated 10 months ago by 37k • written 8.0 years ago by ★ 1.7k
45
votes
35
replies
4.5k
views
12 follow
Forum: looking for a bioinformatics project to do during military rotation
military
updated 7 months ago by 37k • written 5.4 years ago by ▴ 60
65
votes
35
replies
18k
views
17 follow
Which Dna Compression Algorithms Are Actually Used?
dna
updated 5 months ago by 152k • written 11.7 years ago by ▴ 270
25
votes
35
replies
28k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 6 days ago by ▴ 10 • written 8.9 years ago by ★ 4.0k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 6 months ago by 37k • written 4.6 years ago by ★ 1.3k
143
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation maf tcga cancer music Tutorial
updated 9 months ago by 37k • written 9.8 years ago by 5.8k
80
votes
34
replies
3.9k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 4 weeks ago by 37k • written 7.7 years ago by ▴ 500
16
votes
34
replies
11k
views
6 follow
Why am I unable to load my data from a tab separated file into R?
microarray programming R
updated 9 months ago by 37k • written 8.0 years ago by ▴ 920
41
votes
34
replies
9.1k
views
7 follow
Technical replicates in RNAseq
RNA-Seq technical_replicates
11 months ago by grant.hovhannisyan ★ 2.5k
15
votes
34
replies
10k
views
Improving efficiency of awk for large files
awk
updated 3 months ago by 37k • written 7.5 years ago by ▴ 350
62
votes
34
replies
23k
views
20 follow
Phylogenetic Analysis Of Whole Genomes
phylogenetics tree
updated 11 months ago by 37k • written 12.5 years ago by ▴ 120
19
votes
34
replies
4.2k
views
6 follow
How can I convert the blast results into a matrix?
perl linux python blast
updated 11 months ago by 37k • written 8.2 years ago by ▴ 150
68
votes
33
replies
15k
views
18 follow
Choosing Random Set Of Seqs From Larger Set
random fasta
updated 9 months ago by 37k • written 10.9 years ago by ▴ 190
12
votes
33
replies
6.5k
views
9 follow
Back-filling missing genotypes in merged VCF
vcf
updated 6 weeks ago by 152k • written 8.2 years ago by ★ 1.0k
126
votes
33
replies
51k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 3 months ago by 37k • written 8.8 years ago by ▴ 480
53
votes
32
replies
11k
views
13 follow
Bio-Javascript?
updated 9 months ago by 37k • written 12.0 years ago by ★ 3.1k
88
votes
32
replies
8.1k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 10 months ago by 37k • written 8.3 years ago by 152k
129
votes
32
replies
121k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 10 months ago by 37k • written 11.9 years ago by ▴ 530
70
votes
31
replies
24k
views
10 follow
Illumina Instrument Type from fastq?
fastq
updated 5 months ago by 125k • written 6.6 years ago by 6.5k
93
votes
31
replies
94k
views
20 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 11 months ago by ▴ 60 • written 10.7 years ago by ▴ 380
7
votes
31
replies
13k
views
Scale and Center [normalized] RNA-seq expression counts for PCA ?
sequencing pca genome R RNA-Seq
updated 9 months ago by 37k • written 8.0 years ago by ▴ 250
94
votes
31
replies
36k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python alignment next-gen sequencing database
updated 10 months ago by 37k • written 12.5 years ago by ▴ 280
45
votes
31
replies
8.0k
views
6 follow
What Improvements Would You Recommend For This Genome Scaffolding Software?
genome scaffolding next-gen-sequencing
updated 6 months ago by 37k • written 11.9 years ago by ★ 1.8k
3
votes
31
replies
2.3k
views
Extract reads from BAM file with known variant
bam variant samtools
6 months ago by pablo ▴ 230
12
votes
31
replies
4.5k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
gene geneset abinitio Tutorial genome
3 months ago by Juke34 7.5k
116
votes
31
replies
35k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 7 months ago by 37k • written 9.5 years ago by 11k
97
votes
31
replies
80k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 6 months ago by 37k • written 11.6 years ago by ★ 5.0k
89
votes
31
replies
11k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs visualization genomics
updated 6 months ago by 37k • written 10.9 years ago by ★ 1.5k
2
votes
30
replies
9.3k
views
6 follow
Genomic Restriction Finder
fasta
updated 11 months ago by 37k • written 9.2 years ago by ▴ 20
61
votes
30
replies
30k
views
13 follow
Remove mitochondrial reads from BAM files
awk samtools BAM RNA-Seq
updated 10 months ago by 37k • written 8.0 years ago by ▴ 880
41
votes
30
replies
21k
views
24 follow
Is There A List Of Top N Bioinformatics Or Genome Software Company Or Studio ?
genome software
updated 6 months ago by 37k • written 11.6 years ago by ▴ 190
17
votes
30
replies
28k
views
8 follow
Getting A Vcf File From A Fasta Alignment
vcf fasta conversion alignment
updated 9 months ago by 37k • written 8.9 years ago by ★ 1.1k
21,408 results • Page 2 of 429
Recent Votes
Answer: How can I convert this pairwise format to fasta?
Answer: How can I convert this pairwise format to fasta?
Piping bowtie2 output directly into BAM
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: RNA Editing data from RNA-seq
Comment: RNA Editing data from RNA-seq
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Recent Replies
Answer: What type of database does gnomAD use? by Jeremy Leipzig 21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset by Basti ★ 1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Virtual box by Ram 37k
This post does not fit the theme of this forum.
Comment: Filter InterProScan output for a specific function by jv ▴ 780
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data? by STARDUST • 0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans by GenoMax 125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs. by jv ▴ 780
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf> - Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content by jv ▴ 780
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content by GenoMax 125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
Comment: RNA Editing data from RNA-seq by Genetics • 0
Thank you so much for your kind reply and for helping a bioinformatics beginner like me. Can I use **bowtie2** tools for allignment and th…
Comment: fastqc: Per base sequence content by khoojj • 0
Yes, I have proceed with analysis but I wonder if it is necessary to remove the first 10 or so bp from the reads. I have checked that NEBN…
Comment: Novogene somatic results with GATK mutect2 by GenoMax 125k
Did you look in the header of the provided VCF to see if any information has been encoded there (e.g. command line/options used).
Comment: RNASeq differential expression masked by pathways disregulation by Gama313 ▴ 110
That's exactly what I've done. However the dispersion is really high (primary samples) and the total number of samples seems really low to…
Comment: fastqc: Per base sequence content by GenoMax 125k
If the library was made using tagmentation then you will see that pattern. Flag warnings on FastQC do not immediately indicate that the da…
Answer: What type of database does gnomAD use? by Matthias Zepper 2.9k
I suppose there are multiple? Queries via Hail are very likely run against a [Matrix Table][1], but the web application likely uses a diffe…
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