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119,114 results • Page 2 of 2383
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151
votes
39
replies
26k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 19 months ago by 44k • written 11.7 years ago by 3.0k
151
votes
70
replies
54k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 13 months ago by ▴ 260 • written 6.9 years ago by 88k
150
votes
33
replies
142k
views
27 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 19 days ago by 44k • written 12.6 years ago by ★ 2.9k
149
votes
35
replies
63k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 19 months ago by 44k • written 11.9 years ago by ★ 1.6k
148
votes
33
replies
71k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 23 months ago by 44k • written 10.5 years ago by ▴ 520
147
votes
34
replies
56k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 19 months ago by 44k • written 11.5 years ago by 6.1k
145
votes
56
replies
9.4k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 20 months ago by 44k • written 11.5 years ago by 101k
144
votes
14
replies
23k
views
15 follow
What Are The Classic Papers In Bioinformatics?
literature papers history
updated 3.5 years ago by 22k • written 14.0 years ago by 18k
144
votes
62
replies
12k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 20 months ago by 44k • written 13.6 years ago by ★ 2.9k
143
votes
14
replies
171k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 11 months ago by 44k • written 14.5 years ago by 164k
143
votes
33
replies
32k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 5.5 years ago by ▴ 50 • written 14.3 years ago by 13k
142
votes
21
replies
31k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 2.4 years ago by 44k • written 9.8 years ago by ★ 1.6k
142
votes
22
replies
72k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 16 months ago by 88k • written 6.9 years ago by ★ 1.9k
140
votes
18
replies
34k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq alignment next-gen R assembly
updated 8 months ago by 44k • written 5.1 years ago by ▴ 810
139
votes
25
replies
86k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 2.5 years ago by 44k • written 12.5 years ago by ★ 4.3k
138
votes
21
replies
72k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
4.0 years ago by Malachi Griffith 20k
138
votes
42
replies
22k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 18 months ago by 4.5k • written 11.4 years ago by ★ 1.6k
136
votes
29
replies
8.1k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 2.5 years ago by 44k • written 13.8 years ago by 22k
136
votes
26
replies
25k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix perl genomics
updated 20 months ago by 44k • written 12.8 years ago by ▴ 300
136
votes
18
replies
174k
views
16 follow
Blast - Formatting Output
blast format output
updated 22 months ago by ▴ 30 • written 10.8 years ago by ▴ 320
135
votes
27
replies
47k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.5 years ago by 44k • written 12.5 years ago by 33k
134
votes
65
replies
7.0k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 16 months ago by 44k • written 4.9 years ago by ▴ 920
134
votes
123
replies
41k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 19 months ago by ★ 1.2k • written 6.0 years ago by 88k
131
votes
44
replies
37k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 19 months ago by 44k • written 8.1 years ago by ★ 1.1k
131
votes
48
replies
17k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 13.2 years ago by ★ 2.6k • written 13.2 years ago by 11k
131
votes
19
replies
187k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 3.5 years ago by • 0 • written 12.3 years ago by ▴ 370
130
votes
37
replies
14k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 13.1 years ago by ★ 1.3k • written 13.1 years ago by ▴ 820
129
votes
25
replies
88k
views
20 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 3 months ago by • 0 • written 11.4 years ago by ▴ 390
129
votes
33
replies
132k
views
31 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 4 months ago by • 0 • written 13.6 years ago by ▴ 540
129
votes
38
replies
9.6k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 16 months ago by 44k • written 5.5 years ago by 101k
128
votes
83
replies
15k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression fastq-compressor
updated 15 months ago by 44k • written 7.5 years ago by ★ 2.8k
126
votes
56
replies
108k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 12 months ago by ▴ 40 • written 10.3 years ago by ▴ 380
126
votes
46
replies
52k
views
21 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 18 months ago by 44k • written 8.6 years ago by ★ 3.2k
124
votes
29
replies
40k
views
11 follow
PCA in a RNA seq analysis
RNA-Seq pca
updated 5.9 years ago by 28k • written 7.0 years ago by ▴ 330
124
votes
13
replies
179k
views
13 follow
How Can I Convert Bam To Sam?
bam next-gen-sequencing sam
updated 13 months ago by 44k • written 14.3 years ago by 5.0k
124
votes
35
replies
45k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 17 months ago by 44k • written 7.3 years ago by ▴ 830
124
votes
29
replies
7.8k
views
18 follow
What License Do You Use When You Release Code And Data?
software general subjective
updated 11 months ago by 44k • written 14.6 years ago by 7.4k
123
votes
7
replies
124k
views
Bam And Indexed Bam Files
bam index
12.8 years ago by Sahel ▴ 260
122
votes
31
replies
207k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 11 months ago by 44k • written 14.5 years ago by 11k
122
votes
17
replies
78k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 2.6 years ago by 44k • written 13.5 years ago by ▴ 370
122
votes
44
replies
12k
views
24 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 11 months ago by 44k • written 11.9 years ago by 101k
121
votes
44
replies
22k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 20 months ago by 44k • written 14.3 years ago by 5.3k
121
votes
33
replies
40k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 17 months ago by ★ 2.6k • written 11.1 years ago by 11k
120
votes
8
replies
81k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 2.8 years ago by 44k • written 10.1 years ago by ▴ 540
120
votes
23
replies
32k
views
14 follow
Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
cram bam io hdf
updated 3.5 years ago by 44k • written 10.3 years ago by ▴ 320
119
votes
25
replies
125k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 7.7 years ago by ▴ 170 • written 14.2 years ago by 5.0k
118
votes
15
replies
106k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 13.7 years ago by • 0 • written 13.9 years ago by ▴ 210
118
votes
74
replies
48k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 23 months ago by 146k • written 13.9 years ago by ★ 3.3k
118
votes
26
replies
37k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 19 months ago by ▴ 230 • written 9.4 years ago by ▴ 610
117
votes
66
replies
48k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 19 months ago by 44k • written 6.3 years ago by 85k
119,114 results • Page 2 of 2383
Recent Votes
Comment: Associating VDJ clonotyping data with scRNA-seq in Seurat
A: Change sample names in vcf
Answer: why do I get this error while reading single cell RNA seq data in R
A: Is there a tool that can output the raw genotype call (i.e., 0/1) rather than th
Answer: Unexpected High T-Base Content in scRNA-seq Fastq Files and GC Bias Correction
cnv_facets run problem
Answer: why do I get this error while reading single cell RNA seq data in R
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Popular Question to atakanekiz ▴ 310
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Recent Replies
Comment: miRNA mapping with bowtie2 gives low alignment % by Ant ▴ 10
Hi, I used bowtie1 1.3.1 and it increased a little, but it wasn't very satisfactory. I used the parameters: `bowtie -n 0 -l 15 -e 99999 -…
Comment: Merge VCF files by chromosome and Across samples by Maverick ▴ 10
Hi, My assumption was combine and genotype had to be done for the whole vcf file and so I merged them first. So the joint calling isn't …
Comment: Merge VCF files by chromosome and Across samples by Pierre Lindenbaum 164k
why calling CombineGVCFs with merged vcfs when you could combine+genotype each chromosome ?
Answer: cnvpytor run problem by yura.grabovska ▴ 520
Where are you running this analysis? Do you have sufficient memory to run the analysis. You might be running out of resources. Are you runn…
Comment: Merge VCF files by chromosome and Across samples by Pierre Lindenbaum 164k
> (no matter what tool I run vcftools, Picard) show us the picard command tool
Answer: PCA for count data by yura.grabovska ▴ 520
Typically a PCA is calculated on a matrix of correlation coefficients so the robustness of a PCA depends on certain assumptions that come w…
Answer: cnv_facets run problem by dariober 14k
cnv_facets currently supports only mouse and human genomes (I know...). I'm in the process of enabling other species, but for the time bein…
Answer: miRNA mapping with bowtie2 gives low alignment % by Kevin ▴ 90
Because the read length goes to 23 bp on average after trimming, I'd guess your library quality is fine and the reads are structured as exp…
Comment: miRNA mapping with bowtie2 gives low alignment % by Ant ▴ 10
okay, I will try and come to tell the results, thanks
Comment: miRNA mapping with bowtie2 gives low alignment % by GenoMax 146k
Try `bowtie v.1.x` since you want ungapped alignments for miRNA.
Comment: Germline variants in Cancer by Ram 44k
> pathogenic You need ClinVar, SIFT and PolyPhen2 annotations. > germline variants Use MuTect2 with [the option `--genotype-germline-sit…
Answer: Does mageck-vispr calculate differently than mageck? by jared.andrews07 ★ 17k
This probably stems from differences in the gene variance modeling (which is set to `--genes-var 0` in the VISPR run. It's `1000` by defaul…
Comment: installing ArchR on a mac by Assa Yeroslaviz ★ 1.9k
I will, thanks.
Comment: Does mageck-vispr calculate differently than mageck? by Assa Yeroslaviz ★ 1.9k
I can't influence the name in `vispr`. Both methods starts with fastq files, only in `mageck` I need to do two steps to runs the `mle` al…
Comment: Unexplainable missing values in single cell Seurat object by Gerard ▴ 10
raw_counts <- seurat_object@assays$RNA@features["geneofinterest", , drop = FALSE] raw_counts_df <- as.data.frame(raw_counts) pr…
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