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1,000 results • Page 4 of 20
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87
votes
25
replies
50k
views
21 follow
How To Split A Multiple Fasta
fasta split
updated 16 months ago by 39k • written 12.8 years ago by ▴ 460
1.2k
votes
206
replies
50k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 6 days ago by ★ 1.2k • written 12.2 years ago by 21k
11
votes
13
replies
49k
views
pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R RNA-Seq pheatmap arg10
updated 2.4 years ago by ▴ 40 • written 2.9 years ago by ▴ 130
50
votes
33
replies
49k
views
10 follow
I would like to add gene names to a volcano plot obtained from DEseq2
RNA-Seq DEseq2 R
updated 5.1 years ago by 85k • written 6.9 years ago by ▴ 320
36
votes
4
replies
49k
views
TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
z-scores TCGA RSEM
updated 2.1 years ago by 39k • written 8.9 years ago by ★ 4.1k
6
votes
7
replies
49k
views
matching and merging data frames of different lengths
R
updated 20 months ago by 39k • written 9.0 years ago by ▴ 900
30
votes
20
replies
49k
views
11 follow
List Of All Transcription Factors In Human
transcription ensembl genes
updated 10.7 years ago by 35k • written 10.7 years ago by ▴ 730
89
votes
21
replies
49k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq read
updated 9.5 years ago by ▴ 240 • written 10.6 years ago by ▴ 270
24
votes
7
replies
49k
views
What Databases Are Available For Rna-Seq Datasets?
rna-seq database geo
updated 11.0 years ago by 18k • written 11.0 years ago by ▴ 140
45
votes
11
replies
49k
views
10 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 10 months ago by 39k • written 7.4 years ago by ▴ 470
60
votes
15
replies
49k
views
11 follow
Estimate Insert Size In Paired-End/Mate-Pair
next-gen sequencing alignment paired
updated 19 months ago by 39k • written 11.4 years ago by ▴ 190
16
votes
8
replies
49k
views
9 follow
Ensembl Ids To Gene Name Conversion
gene ensembl
updated 4.2 years ago by • 0 • written 11.1 years ago by ▴ 30
22
votes
4
replies
48k
views
Convert VCFf file to plink ped/map format while filtering the SNPs
vcftools plink ped map
updated 4.3 years ago by • 0 • written 8.7 years ago by ▴ 350
36
votes
8
replies
48k
views
10 follow
Adding Read Groups To Bam Files
bam gatk samtools bwa
updated 24 months ago by 11k • written 11.0 years ago by 12k
98
votes
12
replies
48k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 2.2 years ago by ▴ 10 • written 11.4 years ago by ▴ 420
87
votes
37
replies
48k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 15 months ago by 39k • written 9.9 years ago by ▴ 110
0
votes
3
replies
48k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 10
45
votes
3
replies
48k
views
Gwas Vs. Qtl Mapping?
gwas mapping
updated 11 months ago by 39k • written 11.0 years ago by ▴ 460
10
votes
4
replies
48k
views
BLAST: Identity % and Similarity %
blast
updated 7.0 years ago by ★ 3.9k • written 7.0 years ago by ▴ 40
4
votes
1
reply
48k
views
In ggplot, assign a variable/category to a specific color?
R ggplot plots colors
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 100
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 4 months ago by 39k • written 9.9 years ago by ★ 3.0k
57
votes
15
replies
47k
views
11 follow
Filtering Vcf File
vcftools vcf snp indel
updated 15 months ago by 39k • written 10.8 years ago by ▴ 830
35
votes
6
replies
47k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 2.0 years ago by ★ 14k • written 3.5 years ago by ▴ 140
66
votes
19
replies
47k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq tools
updated 7 days ago by ▴ 10 • written 10.3 years ago by ★ 3.6k
29
votes
9
replies
47k
views
What Is The Difference Between Sequencing Depth And Coverage
sequencing read coverage
updated 12.2 years ago by 52k • written 12.2 years ago by ▴ 970
88
votes
52
replies
46k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 18 months ago by ▴ 10 • written 5.6 years ago by ▴ 210
13
votes
5
replies
46k
views
7 follow
Obtaining The Snp Rs Number With The Chromosomal Position
r snps bioconductor
updated 20 months ago by ▴ 180 • written 10.1 years ago by ▴ 410
34
votes
5
replies
46k
views
Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about that in an assymmetrical matrix
pheatmap R
updated 3 months ago by 39k • written 6.3 years ago by ▴ 170
29
votes
10
replies
46k
views
How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
fastq paired-end illumina
updated 9.2 years ago by ★ 2.2k • written 9.2 years ago by ▴ 330
52
votes
21
replies
46k
views
11 follow
Fastq Splitter For Paired End Reads
rna paired tool
updated 17 months ago by 39k • written 11.2 years ago by ★ 1.5k
27
votes
11
replies
45k
views
samtools sort bam file
ChIP-Seq
updated 5.0 years ago by 47k • written 5.0 years ago by ▴ 120
39
votes
16
replies
45k
views
10 follow
How to split paired end SRA file into 2 correct fastq files
next-gen sra fastq
updated 16 months ago by ▴ 10 • written 6.6 years ago by ▴ 120
13
votes
14
replies
45k
views
7 follow
Convert SAM to BAM
sam RNA-Seq bam
updated 18 months ago by 39k • written 8.9 years ago by ▴ 80
112
votes
24
replies
45k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 9 months ago by 39k • written 12.1 years ago by ▴ 480
54
votes
52
replies
45k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Tool on Gene Clustering Function based
updated 17 months ago by 39k • written 8.8 years ago by 7.5k
32
votes
19
replies
44k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene convert
updated 5 months ago by 39k • written 10.0 years ago by ▴ 240
125
votes
46
replies
44k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 8 weeks ago by 39k • written 7.3 years ago by ★ 3.2k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
21
votes
5
replies
44k
views
Any Method Of Converting Bigwig File Format Into Bed Format?
bigwig bed
updated 4.0 years ago by ▴ 190 • written 10.1 years ago by ▴ 50
21
votes
11
replies
44k
views
reading a bed file in R
bed R
updated 18 months ago by 39k • written 7.5 years ago by ★ 4.2k
46
votes
15
replies
44k
views
11 follow
How to extract specific chromosome from vcf file
vcf
updated 8 months ago by ▴ 530 • written 6.9 years ago by ★ 2.0k
2
votes
3
replies
44k
views
Convert text file to VCF file ?
vcf
updated 4.1 years ago by 11k • written 8.3 years ago by ▴ 260
30
votes
10
replies
44k
views
Filtering A Sam File For Quality Scores
sam
updated 11.1 years ago by 11k • written 11.1 years ago by ★ 1.3k
5
votes
3
replies
44k
views
Extract the values by matching two rows of one dataframe with the two columns of another dataframe
dataframe match
updated 12 months ago by 39k • written 8.2 years ago by ★ 2.0k
48
votes
4
replies
44k
views
How To Convert The Bed File To Ped File
bed ped
updated 9 months ago by • 0 • written 12.8 years ago by ▴ 310
41
votes
7
replies
44k
views
How to extract sample id using bcftools or vcftools
SNP vcf bcftools vcftools
updated 22 months ago by ▴ 260 • written 8.1 years ago by ▴ 510
6
votes
12
replies
44k
views
9 follow
Opening A Fasta File In Windows
fasta blast makeblastdb
updated 11.2 years ago by • 0 • written 11.3 years ago by • 0
77
votes
18
replies
44k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 10 months ago by • 0 • written 13.0 years ago by ★ 1.1k
17
votes
5
replies
44k
views
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
heatmap r
updated 11.5 years ago by 52k • written 11.5 years ago by ▴ 140
17
votes
3
replies
44k
views
What'S The Meaning Of "Bridge Pcr" In The Next Generation Sequencing
pcr sequencing
updated 9.9 years ago by ★ 5.2k • written 9.9 years ago by ▴ 130
1,000 results • Page 4 of 20
Recent Votes
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
Answer: Alignment of case vs. control from different origin
Comment: Alignment of case vs. control from different origin
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Recent Replies
Comment: Differential protein expression analysis by Ribo ▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
No, your code isn't correct. You are testing an intercept equal to zero instead of testing for a logFC. I wonder what comparison you were t…
Answer: Extract sequences from a fastq file by a list of IDs by GenoMax 129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. These are raw counts.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Ayish • 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix? by Thu • 0
Hi! Thanks for sharing your solution! It works! :)
Comment: Gene prediction software by Darked89 4.4k
Looks like there are five Clarias genomes: * https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp] The most complete seems t…
Comment: Alignment of case vs. control from different origin by sativus ▴ 10
Again, thank you so much for these very clearly explained summaries. After reading some articles on the matter, i feel i have a much better…
Answer: Extract sequences from a fastq file by a list of IDs by colindaven 4.9k
Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
Comment: Extract sequences from a fastq file by a list of IDs by Pierre Lindenbaum 154k
> but none of them work for me https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs by Pierre Lindenbaum 154k
https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
I have tried this one before but the output file is empty
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
I have tried all of them but none of them work for me
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