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1,000 results • Page 2 of 20
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40
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15
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65k
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14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix conversion entrez
updated 5 months ago by 38k • written 9.7 years ago by ▴ 140
111
votes
25
replies
64k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 7 weeks ago by ▴ 10 • written 12.2 years ago by 153k
35
votes
9
replies
64k
views
8 follow
Minor allele frequency calculation
SNP next-gen
updated 10 months ago by 38k • written 8.4 years ago by ▴ 50
51
votes
15
replies
63k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization software
updated 11 months ago by 38k • written 11.8 years ago by ▴ 70
40
votes
7
replies
62k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r rna heatmap clustering gene
updated 9 months ago by 38k • written 11.4 years ago by ▴ 450
50
votes
15
replies
62k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts sequence fastq
updated 6 weeks ago by 38k • written 11.8 years ago by ★ 1.7k
53
votes
4
replies
61k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence next-gen-sequencing
updated 5 months ago by 38k • written 8.4 years ago by ▴ 800
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment tool
updated 9 months ago by 38k • written 13.1 years ago by ★ 1.0k
152
votes
24
replies
59k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing tools rna-seq alternative-splicing
updated 8 months ago by 38k • written 10.1 years ago by 10k
361
votes
57
replies
59k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 6 months ago by 84k • written 13.1 years ago by 97k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 14 days ago by 38k • written 2.7 years ago by ▴ 690
26
votes
10
replies
59k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 19 days ago by 38k • written 2.0 years ago by ★ 1.3k
11
votes
9
replies
58k
views
7 follow
combining fasta files
windows fasta notepad
updated 4 months ago by • 0 • written 8.2 years ago by ▴ 30
2
votes
10
replies
58k
views
R: remove rows by a list of rownames
R
updated 11 months ago by 38k • written 8.2 years ago by ▴ 50
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 4 weeks ago by 38k • written 10.3 years ago by ★ 1.6k
88
votes
18
replies
58k
views
12 follow
Sequence length from Fasta
fasta
updated 3 months ago by 38k • written 8.4 years ago by ▴ 80
328
votes
54
replies
57k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 6 months ago by 84k • written 13.0 years ago by 24k
91
votes
25
replies
57k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 6 months ago by 52k • written 12.1 years ago by 3.4k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 11 months ago by 38k • written 11.9 years ago by ★ 3.4k
49
votes
20
replies
56k
views
14 follow
Bam Header Edit
bam
updated 7 months ago by 38k • written 10.8 years ago by 12k
62
votes
22
replies
56k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 3 months ago by • 0 • written 10.4 years ago by ★ 1.5k
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 10 months ago by ▴ 20 • written 12.6 years ago by ★ 2.6k
80
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 29 days ago by 38k • written 9.8 years ago by 11k
127
votes
33
replies
53k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 5 months ago by 38k • written 8.9 years ago by ▴ 480
1
vote
6
replies
53k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 11 days ago by 38k • written 6.2 years ago by • 0
74
votes
24
replies
52k
views
16 follow
How To Sort Bed Format File
bed
updated 5 months ago by 153k • written 10.1 years ago by ▴ 430
27
votes
8
replies
51k
views
7 follow
R: How to convert log2FC (Fold Change) obtained by limma's topTable() function to FC
limma microarray topTable R
updated 8 months ago by 38k • written 8.9 years ago by ★ 4.1k
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 4 weeks ago by 38k • written 10.0 years ago by 5.9k
26
votes
21
replies
50k
views
9 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 4 weeks ago by 38k • written 9.9 years ago by ▴ 90
48
votes
19
replies
49k
views
11 follow
How Can I Convert Bam/Sam To Wiggle
wiggle perl samtools
updated 20 days ago by 38k • written 12.5 years ago by ★ 1.4k
75
votes
22
replies
49k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 5 days ago by 38k • written 9.1 years ago by ★ 1.5k
77
votes
27
replies
49k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 7 months ago by ▴ 70 • written 9.3 years ago by ▴ 180
54
votes
22
replies
48k
views
14 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 8 months ago by 34k • written 10.1 years ago by ★ 1.2k
1.2k
votes
205
replies
48k
views
107 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 10 weeks ago by ▴ 250 • written 12.0 years ago by 21k
45
votes
3
replies
48k
views
Gwas Vs. Qtl Mapping?
gwas mapping
updated 9 months ago by 38k • written 10.8 years ago by ▴ 460
65
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 weeks ago by 38k • written 9.8 years ago by ★ 3.0k
45
votes
11
replies
47k
views
10 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 7 months ago by 38k • written 7.2 years ago by ▴ 470
66
votes
18
replies
46k
views
16 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq tools
updated 16 days ago by • 0 • written 10.1 years ago by ★ 3.6k
112
votes
24
replies
45k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 6 months ago by 38k • written 11.9 years ago by ▴ 480
34
votes
5
replies
44k
views
Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about that in an assymmetrical matrix
pheatmap R
updated 6 weeks ago by 38k • written 6.1 years ago by ▴ 170
32
votes
19
replies
44k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene convert
updated 12 weeks ago by 38k • written 9.8 years ago by ▴ 240
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 10 months ago by 38k • written 8.1 years ago by ★ 2.0k
77
votes
18
replies
43k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 7 months ago by • 0 • written 12.9 years ago by ★ 1.1k
48
votes
4
replies
43k
views
How To Convert The Bed File To Ped File
bed ped
updated 6 months ago by • 0 • written 12.6 years ago by ▴ 310
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 15 days ago by 38k • written 5.3 years ago by 84k
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 7 weeks ago by 38k • written 7.9 years ago by ★ 2.0k
31
votes
7
replies
42k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq deseq2 tpm
updated 8 months ago by 38k • written 8.1 years ago by ▴ 170
32
votes
10
replies
42k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat illumina strand
updated 5 months ago by 38k • written 10.1 years ago by 10k
38
votes
14
replies
42k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl fasta python parsing
updated 11 months ago by 52k • written 11.2 years ago by ▴ 350
116
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 4 months ago by 127k • written 12.3 years ago by ★ 3.2k
1,000 results • Page 2 of 20
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Answer: Scaling RNA-Seq data before clustering?
Answer: How to use CAFE from Orthofinder Results
Answer: merge vcf.gz file
STAR solo set parameters for scrna-seq
STAR solo set parameters for scrna-seq
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Comment: merge vcf.gz file by Mali • 0
file1 = '/sci/labs/orzuk/orzuk/projects/Skin/data/Ichilov/vcfFiles/vcfFiles/eb3_1001_748-gatk-haplotype.final.vcf.gz' file2 = '/sci/labs/or…
Comment: Which GPU for local Colabfold by matt_arnold_bio • 0
Another giveaway is that when you hit run, it will say either "Running on GPU" or "Running on CPU" in the log output... ![enter image desc…
Answer: Which GPU for local Colabfold by matt_arnold_bio • 0
Hi Arjen, This is a little while ago now so maybe this is not that helpful but... You should be able to tell if the GPU is being seen…
Comment: STAR solo set parameters for scrna-seq by t.ru ▴ 20
it's single cell mars-seq. Yes sorry its a fastq file.
Answer: boxplot issue by yura.grabovska ▴ 50
First of all, you're not outputting the result of your scale to anything... t(apply(mat, 1, scale)) colnames(mat) <- rownames(cold…
Comment: STAR solo set parameters for scrna-seq by GenoMax 127k
> a fasta file similar to this This is not a fasta file It is a fastq format file. Are you sure this is single cell RNAseq data? Looking…
Answer: heatmap issue by yura.grabovska ▴ 50
Your controls clearly show variable expression for the genes you're plotting so to get them to stick together on the left, you would need t…
Comment: How to demultiplex single end - dual index run - NextSeq 500 by GenoMax 127k
Correct. This is a single-end dual indexed (8 bp each) run.
Comment: genome annotation [sstart] [send] - how to get protein sequence from gene by danfarkas • 0
Hi shenwei356, Thanks for the clarification. However, I did try this, and it was not yielding the expected amino acid sequences. This is w…
Comment: Artificial reads - remove multiple mapped reads against reference genome, and on by Agamemnon ▴ 60
I ran ```samtools view -F 4 -q 42 test.bam | wc -l``` and I get ```6159141```, why is there a discrepancy, as originally only ```5200484```…
Comment: differential gene analysis by kalyani • 0
okay thankks!
Comment: Kallisto bustools for scRNA-seq by t.ru ▴ 20
@SRR17050039.1 NB501465:544:HF2H7BGXB:1:22104:14442:1233_TCCTGAGC_barcode=NA-EEEE-AAAAAEE-EEEEEEEE-GCTG-TGCCAGA-ACGTTCAT-W202012/1 GCCCTGTA…
Comment: merge vcf.gz file by Pierre Lindenbaum 153k
"file 1 " , with a space, cannot be a real argument. show us the real filenames please, and the error messages.
Answer: merge vcf.gz file by ATpoint 70k
You must compress with bgzip. gzip -d your.vcf.gz bgzip your.vcf
Comment: GO enrichment analysis by hellokwmin • 0
Thank you for your reply. Unfortunately, the organism I am using is non-model organism (i.e. one of plant species). So, with the informati…
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