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114,007 results • Page 3 of 2281
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1
vote
3
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64k
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Error in loading R package "GO.db" in installing WGCNA R package
R
updated 19 months ago by 41k • written 8.8 years ago by ▴ 10
40
votes
7
replies
63k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r rna heatmap clustering gene
updated 17 months ago by 41k • written 12.1 years ago by ▴ 450
36
votes
14
replies
62k
views
9 follow
What Is The Difference Between Hg18 And Hg19?
genome hg hg
updated 11.8 years ago by 14k • written 11.8 years ago by ▴ 170
62
votes
22
replies
62k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 12 months ago by • 0 • written 11.1 years ago by ★ 1.5k
137
votes
33
replies
62k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 13 months ago by 41k • written 9.6 years ago by ▴ 480
25
votes
5
replies
62k
views
7 follow
Rpkm Calculation For Genes
rpkm rna-seq
updated 11.1 years ago by 13k • written 11.1 years ago by ▴ 270
328
votes
54
replies
62k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 4 weeks ago by 41k • written 13.7 years ago by 24k
157
votes
24
replies
61k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing splicing rna-seq
updated 5 months ago by 41k • written 10.8 years ago by 10k
149
votes
35
replies
61k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 9 months ago by 41k • written 11.0 years ago by ★ 1.6k
102
votes
30
replies
61k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 6 weeks ago by 41k • written 13.8 years ago by ★ 1.0k
91
votes
25
replies
60k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 15 months ago by 53k • written 12.8 years ago by 3.4k
100
votes
6
replies
60k
views
6 follow
Insert Size And Fragment Size ?
2.1 years ago by Nicolas Rosewick 10k
27
votes
21
replies
60k
views
21 follow
Public Electronic Health Records Database
database
updated 2.2 years ago by 41k • written 10.6 years ago by ★ 1.6k
39
votes
20
replies
60k
views
8 follow
How to convert to .SRA files to .FQ (FASTQ)
fastq FASTQ sra RNA-Seq SRAA
updated 22 months ago by ▴ 20 • written 9.3 years ago by ▴ 50
53
votes
20
replies
60k
views
14 follow
Bam Header Edit
bam
updated 15 months ago by 41k • written 11.5 years ago by 12k
53
votes
8
replies
60k
views
8 follow
What Is A Good Threshold For Log2 Fold Change?
microarray gene
updated 8.8 years ago by 20 • written 12.7 years ago by ▴ 90
1
vote
6
replies
60k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 8 months ago by 41k • written 6.9 years ago by • 0
134
votes
22
replies
59k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 6 months ago by 86k • written 6.0 years ago by ★ 1.9k
90
votes
44
replies
59k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 19 months ago by 41k • written 12.6 years ago by ★ 3.4k
37
votes
5
replies
59k
views
Idenity, e value or bitscore ?
blast annotation
updated 4.5 years ago by ▴ 300 • written 7.6 years ago by ▴ 60
2
votes
10
replies
59k
views
R: remove rows by a list of rownames
R
updated 19 months ago by 41k • written 8.9 years ago by ▴ 50
19
votes
2
replies
59k
views
Keeping pheatmap colour range the same for different data sets
R RNA-Seq pheatmap
updated 7.6 years ago by ▴ 620 • written 7.6 years ago by ▴ 60
17
votes
6
replies
59k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
blast sequence
updated 7 weeks ago by 41k • written 13.8 years ago by ★ 1.4k
76
votes
24
replies
58k
views
16 follow
How To Sort Bed Format File
bed
updated 13 months ago by 158k • written 10.8 years ago by ▴ 450
164
votes
70
replies
58k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 11.9 years ago by ▴ 430 • written 12.4 years ago by ★ 1.8k
93
votes
19
replies
58k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 5 months ago by 41k • written 13.2 years ago by ★ 2.6k
13
votes
13
replies
58k
views
pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R RNA-Seq pheatmap arg10
updated 2.9 years ago by ▴ 40 • written 3.4 years ago by ▴ 160
7
votes
3
replies
57k
views
what is the difference between single end and paired end in sequencing
RNA-Seq
updated 2.1 years ago by 41k • written 9.5 years ago by ▴ 650
85
votes
2
replies
57k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by 41k • written 10.4 years ago by 11k
50
votes
5
replies
56k
views
6 follow
Subsampling Bam File With Samtools
samtools bam
updated 2.2 years ago by ▴ 60 • written 10.4 years ago by ▴ 250
48
votes
10
replies
56k
views
7 follow
RNA-seq: Explain STAR quantMode geneCounts values
RNA-Seq STAR Differential expression
updated 5.7 years ago by ▴ 530 • written 7.1 years ago by ▴ 370
38
votes
41
replies
56k
views
9 follow
Volcano Plot from DEseq2
R
written 6.1 years ago by ★ 1.1k
0
votes
6
replies
56k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
R heatmap error
updated 2.5 years ago by • 0 • written 4.7 years ago by ▴ 50
64
votes
24
replies
56k
views
20 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 22 months ago by 41k • written 10.9 years ago by ▴ 290
15
votes
5
replies
55k
views
R Help: For Loop Over Range Of Number And Calculate Average Using An If Statement
r
updated 7.9 years ago by 20 • written 9.8 years ago by ▴ 110
29
votes
11
replies
55k
views
samtools sort bam file
ChIP-Seq
updated 5.5 years ago by 47k • written 5.5 years ago by ▴ 120
65
votes
12
replies
55k
views
7 follow
Recommended cutoff for FDR - 0.05 or 0.1
RNA-Seq R
updated 2.7 years ago by • 0 • written 7.3 years ago by ▴ 180
1.2k
votes
206
replies
55k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 6 months ago by ★ 1.3k • written 12.7 years ago by 22k
12
votes
7
replies
55k
views
Use Python To List Filename With Specific Extensions.
python
updated 12.5 years ago by 28k • written 12.5 years ago by ★ 1.7k
72
votes
18
replies
55k
views
13 follow
Extracting Multiple Fasta Sequences At A Time From A File Containing Many Sequences
fasta sequence parsing perl
updated 13.2 years ago by 6.0k • written 13.2 years ago by ▴ 110
16
votes
14
replies
55k
views
7 follow
Convert SAM to BAM
sam RNA-Seq bam
updated 24 months ago by 41k • written 9.4 years ago by ▴ 90
28
votes
22
replies
55k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 5 months ago by • 0 • written 10.6 years ago by ▴ 90
30
votes
8
replies
54k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma microarray topTable R
updated 17 months ago by 41k • written 9.6 years ago by ★ 4.1k
86
votes
12
replies
54k
views
9 follow
What are chimeric reads?
sequence
updated 22 months ago by 41k • written 9.1 years ago by ▴ 300
61
votes
23
replies
54k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 16 days ago by ★ 1.2k • written 10.8 years ago by ★ 1.3k
78
votes
27
replies
54k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 15 months ago by ▴ 70 • written 10.0 years ago by ▴ 190
40
votes
9
replies
54k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 4 months ago by ▴ 160 • written 4.0 years ago by ▴ 140
95
votes
5
replies
53k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools clipped-reads soft-clip bam hard-clip
updated 24 months ago by 41k • written 9.3 years ago by ★ 2.5k
49
votes
13
replies
53k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 10 weeks ago by ▴ 160 • written 7.9 years ago by ▴ 490
42
votes
26
replies
53k
views
11 follow
How To Interpret A T-Test Output Produced By R
statistics
updated 10.4 years ago by 20 • written 11.4 years ago by ★ 1.8k
114,007 results • Page 3 of 2281
Recent Votes
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
Answer: Read count vs Depth
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Recent Replies
Comment: Normalization of RNA captureSeq data (<20 genes captured) by ATpoint 78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen by j.gleixner • 0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
Comment: Where to download excel file to include major human disease, prevalence and inci by GenoMax 136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci by Pierre Lindenbaum 158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline by ju_ra • 0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms? by Elisabeth Gasteiger ★ 2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by Pierre Lindenbaum 158k
again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out by analyst ▴ 10
Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
Answer: gatk SelectVariants is giving error while extracting SNPs out of vcf file by Pierre Lindenbaum 158k
This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
Comment: gatk SelectVariants is giving error while extracting SNPs out of vcf file by analyst ▴ 10
I observed that my reference genomic fasta file contains both lower case and upper case nucleotides. Do I need to convert lower case nucle…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
I observed that both lower and upper cases are present in reference fasta file. Is bbtool case sensitive that while calling variants it con…
Comment: Read count vs Depth by Mary • 0
Thanks Brain Bushnell Referring to my query1: So u mean that for a particular gene, if total read count is 6, then depth may be just 1 or …
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