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1,000 results • Page 3 of 20
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36
votes
14
replies
60k
views
9 follow
What Is The Difference Between Hg18 And Hg19?
genome hg hg
updated 11.3 years ago by 14k • written 11.3 years ago by ▴ 170
91
votes
18
replies
60k
views
12 follow
Sequence length from Fasta
fasta
updated 5 months ago by 39k • written 8.6 years ago by ▴ 80
102
votes
30
replies
60k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment tool
updated 11 months ago by 39k • written 13.2 years ago by ★ 1.0k
155
votes
24
replies
59k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing tools rna-seq alternative-splicing
updated 10 months ago by 39k • written 10.2 years ago by 10k
48
votes
17
replies
59k
views
11 follow
Extract fasta sequences from a file using a list in another file.
fasta header extract awk grep
updated 2.4 years ago by ▴ 450 • written 5.0 years ago by ▴ 50
148
votes
35
replies
59k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 1.6k
2
votes
10
replies
58k
views
R: remove rows by a list of rownames
R
updated 13 months ago by 39k • written 8.3 years ago by ▴ 50
17
votes
6
replies
58k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
sequence blast
updated 2.8 years ago by • 0 • written 13.3 years ago by ★ 1.4k
328
votes
54
replies
58k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 8 months ago by 85k • written 13.2 years ago by 24k
27
votes
21
replies
58k
views
21 follow
Public Electronic Health Records Database
database
updated 20 months ago by 39k • written 10.1 years ago by ★ 1.6k
91
votes
25
replies
58k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 8 months ago by 52k • written 12.3 years ago by 3.4k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 13 months ago by 39k • written 12.1 years ago by ★ 3.4k
62
votes
22
replies
57k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 5 months ago by • 0 • written 10.6 years ago by ★ 1.5k
53
votes
8
replies
57k
views
8 follow
What Is A Good Threshold For Log2 Fold Change?
microarray gene
updated 8.2 years ago by 20 • written 12.2 years ago by ▴ 90
49
votes
20
replies
57k
views
14 follow
Bam Header Edit
bam
updated 9 months ago by 39k • written 11.0 years ago by 12k
38
votes
20
replies
57k
views
8 follow
How to convert to .SRA files to .FQ (FASTQ)
fastq FASTQ sra RNA-Seq SRAA
updated 15 months ago by ▴ 20 • written 8.8 years ago by ▴ 50
7
votes
3
replies
57k
views
what is the difference between single end and paired end in sequencing
RNA-Seq
updated 19 months ago by 39k • written 8.9 years ago by ▴ 600
100
votes
6
replies
57k
views
6 follow
Insert Size And Fragment Size ?
18 months ago by Nicolas Rosewick 10k
93
votes
19
replies
56k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree tool phylogenetics viewer
updated 12 months ago by ▴ 20 • written 12.7 years ago by ★ 2.6k
164
votes
70
replies
55k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 11.4 years ago by ▴ 430 • written 11.9 years ago by ★ 1.8k
36
votes
5
replies
55k
views
Idenity, e value or bitscore ?
blast annotation
updated 4.0 years ago by ▴ 260 • written 7.1 years ago by ▴ 60
127
votes
33
replies
55k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 7 months ago by 39k • written 9.1 years ago by ▴ 480
15
votes
5
replies
55k
views
R Help: For Loop Over Range Of Number And Calculate Average Using An If Statement
r
updated 7.4 years ago by 20 • written 9.3 years ago by ▴ 110
19
votes
2
replies
55k
views
Keeping pheatmap colour range the same for different data sets
R RNA-Seq pheatmap
updated 7.0 years ago by ▴ 620 • written 7.0 years ago by ▴ 60
1
vote
6
replies
54k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 10 weeks ago by 39k • written 6.4 years ago by • 0
12
votes
7
replies
54k
views
Use Python To List Filename With Specific Extensions.
python
updated 11.9 years ago by 27k • written 11.9 years ago by ★ 1.7k
74
votes
24
replies
54k
views
16 follow
How To Sort Bed Format File
bed
updated 7 months ago by 154k • written 10.3 years ago by ▴ 430
72
votes
18
replies
54k
views
13 follow
Extracting Multiple Fasta Sequences At A Time From A File Containing Many Sequences
fasta sequence parsing perl
updated 12.6 years ago by 6.0k • written 12.6 years ago by ▴ 110
80
votes
2
replies
54k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 12 weeks ago by 39k • written 9.9 years ago by 11k
62
votes
24
replies
53k
views
20 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 16 months ago by 39k • written 10.4 years ago by ▴ 290
42
votes
26
replies
53k
views
11 follow
How To Interpret A T-Test Output Produced By R
statistics
updated 9.9 years ago by 20 • written 10.8 years ago by ★ 1.8k
27
votes
8
replies
52k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma microarray topTable R
updated 10 months ago by 39k • written 9.0 years ago by ★ 4.1k
10
votes
8
replies
52k
views
geom_bar plot with several variables
R ggplot2
updated 3.9 years ago by • 0 • written 4.3 years ago by ▴ 450
16
votes
30
replies
52k
views
9 follow
Retrieve The Fasta Nucleic Sequences Of A List Of Ncbi Accession Number Of Proteins
dna sequence retrieval perl bioperl
updated 12.3 years ago by ▴ 290 • written 12.3 years ago by ▴ 90
49
votes
5
replies
52k
views
6 follow
Subsampling Bam File With Samtools
samtools bam
updated 20 months ago by ▴ 40 • written 9.9 years ago by ▴ 250
129
votes
20
replies
52k
views
13 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 3.5 years ago by ▴ 220 • written 5.5 years ago by ★ 1.8k
145
votes
34
replies
52k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 3 months ago by 39k • written 10.1 years ago by 5.9k
26
votes
21
replies
51k
views
9 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 3 months ago by 39k • written 10.1 years ago by ▴ 90
80
votes
27
replies
51k
views
23 follow
Renaming Entries In A Fasta File
fasta
updated 7.1 years ago by ▴ 50 • written 10.7 years ago by ▴ 130
84
votes
12
replies
51k
views
9 follow
What are chimeric reads?
sequence
updated 16 months ago by 39k • written 8.6 years ago by ▴ 290
92
votes
5
replies
51k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools clipped-reads soft-clip bam hard-clip
updated 17 months ago by 39k • written 8.8 years ago by ★ 2.5k
61
votes
12
replies
51k
views
7 follow
Recommended cutoff for FDR - 0.05 or 0.1
RNA-Seq R
updated 2.2 years ago by • 0 • written 6.8 years ago by ▴ 180
77
votes
27
replies
50k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 8 months ago by ▴ 70 • written 9.4 years ago by ▴ 180
10
votes
5
replies
50k
views
Finding number of duplicates in R
R
updated 6.8 years ago by ▴ 280 • written 6.8 years ago by ▴ 60
75
votes
22
replies
50k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 9 weeks ago by 39k • written 9.3 years ago by ★ 1.5k
38
votes
41
replies
50k
views
9 follow
Volcano Plot from DEseq2
R
written 5.6 years ago by ★ 1.1k
48
votes
19
replies
50k
views
11 follow
How Can I Convert Bam/Sam To Wiggle
wiggle perl samtools
updated 11 weeks ago by 39k • written 12.7 years ago by ★ 1.4k
56
votes
22
replies
50k
views
14 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 10 months ago by 35k • written 10.2 years ago by ★ 1.2k
44
votes
10
replies
50k
views
7 follow
RNA-seq: Explain STAR quantMode geneCounts values
RNA-Seq STAR Differential expression
updated 5.1 years ago by ▴ 490 • written 6.6 years ago by ▴ 330
0
votes
6
replies
50k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
R heatmap error
updated 2.0 years ago by • 0 • written 4.2 years ago by ▴ 40
1,000 results • Page 3 of 20
Recent Votes
Answer: Counting intronic reads in bulk RNA-seq
Answer: IGV displays genomic coordinates in a 1-based system or 0-based?
RNAseq expression data log2 transformed has negative values.
Samtools: "Too Many Open Files"
Filtering bad quality probes in illumina microarray data
gene filtering for agilent microarray using Limma
A: Identification Of Significant Differences Between Phylogentic Trees Using Distan
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Recent Replies
Comment: Error while running Megahit by Mensur Dlakic ★ 23k
We can't even begin to guess what the problem was without an error message.
Comment: DEgs RNAseq by dsull ★ 4.2k
Is this single-cell RNAseq or non-single-cell RNAseq? For single-cell, you typically don't do standard "differential gene expression analy…
Comment: Counting intronic reads in bulk RNA-seq by dsull ★ 4.2k
Correct, and I agree -- reads lying fully within introns are usually not counted for either single-cell or bulk. Inclusion of introns in a…
Answer: Counting intronic reads in bulk RNA-seq by swbarnes2 13k
Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.
Answer: Single cell chemistry by swbarnes2 13k
Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
are they distinct transcript IDs but the same gene ID? can you provide any additional context?
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0
that didn't work either
Answer: Why are some WES VCFs larger than others? by Vincent Laufer ★ 2.8k
Hi @kermit and prash (and others)! Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by WouterDeCoster 47k
There is no `:` after `rule fastqc`
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0
sorry that was a typo while i was copying my code! I still get the same error
Comment: too many zeros in 16S rRNA amplicon sequencing data by andres.firrincieli 3.3k
You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post…
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Pierre Lindenbaum 154k
> fastq.gz". what is the dot after `fastq.gz" ` ?
Comment: DownsampleSam by Pierre Lindenbaum 154k
1) I think this is just a warning 2) there must be another error displayed 3) look at samtools view --subsample 4) don't use loops but use…
Comment: ABySS genome assembler by npavliukovec • 0
Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abys…
Comment: desgin a primer for CDS by yuxiang • 0
how can you know the primer is not bind to other gene site? how can you desgin an experiment? I use the FISH to identify the gene, how abo…
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