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1,000 results • Page 2 of 20
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25
votes
9
replies
44k
views
Converting Gff To Bed With Bedtools?
gff bed bedtools
updated 9 weeks ago by 43k • written 11.2 years ago by ▴ 940
35
votes
14
replies
43k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 6 months ago by ▴ 130 • written 7.8 years ago by ★ 5.2k
48
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 11 weeks ago by ▴ 640 • written 7.5 years ago by ▴ 550
121
votes
35
replies
43k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 11 months ago by 43k • written 6.8 years ago by ▴ 810
105
votes
26
replies
42k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 7 months ago by 11k • written 11.3 years ago by ▴ 810
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 7 months ago by ▴ 210 • written 10.2 years ago by ▴ 750
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 5 months ago by 161k • written 14.0 years ago by ▴ 660
121
votes
33
replies
39k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by ★ 2.5k • written 10.6 years ago by 11k
6
votes
25
replies
38k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 10 months ago by • 0 • written 6.1 years ago by ▴ 130
23
votes
4
replies
38k
views
bcftools compressing and indexing vcf files
sequence bcftools vcf index
updated 5 months ago by 141k • written 5.6 years ago by ▴ 270
19
votes
10
replies
38k
views
Ensembl ID to Gene Symbol
gene-symbol
updated 9 months ago by 43k • written 8.0 years ago by ▴ 330
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by ▴ 70 • written 9.8 years ago by ▴ 170
13
votes
6
replies
37k
views
generating genome indexes with STAR
RNA-Seq STAR
updated 9 months ago by ★ 4.3k • written 7.8 years ago by ▴ 80
10
votes
5
replies
37k
views
How to compare 2 VCF files
vcf SNP
updated 9 months ago by 43k • written 9.9 years ago by ▴ 100
80
votes
21
replies
36k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by • 0 • written 10.0 years ago by ▴ 660
21
votes
8
replies
36k
views
8 follow
Merging/Concatenating Vcf Files
vcftools snp indel
updated 7 months ago by ▴ 330 • written 11.7 years ago by ▴ 830
39
votes
16
replies
36k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 3 months ago by 141k • written 3.7 years ago by ▴ 160
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq macs ChIP-Seq peaks
updated 9 months ago by 43k • written 7.6 years ago by 13k
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 5 months ago by 43k • written 14.0 years ago by 161k
33
votes
10
replies
35k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq ensembl
updated 9 months ago by 43k • written 9.8 years ago by ▴ 540
197
votes
27
replies
34k
views
20 follow
Forum: Bioinformatics Cartoon
bioinformatics
updated 9 months ago by 43k • written 12.3 years ago by ★ 2.3k
13
votes
12
replies
34k
views
Estimating Insert Size From Paired End Data.
picard alignment paired-end
updated 6 months ago by 43k • written 10.1 years ago by 12k
20
votes
10
replies
34k
views
6 follow
read depth using samtools
depth samtools
updated 7 months ago by ▴ 10 • written 5.3 years ago by ▴ 30
28
votes
11
replies
34k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools strand
updated 12 weeks ago by • 0 • written 12.4 years ago by ▴ 540
39
votes
23
replies
34k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 7 months ago by ▴ 40 • written 2.8 years ago by ▴ 130
42
votes
16
replies
33k
views
14 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 6 months ago by ★ 1.2k • written 5.1 years ago by ▴ 70
90
votes
48
replies
33k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 5 months ago by 43k • written 10.5 years ago by ★ 7.8k
67
votes
15
replies
33k
views
14 follow
Rna-Seq Pipeline
pipeline next-gen-sequencing rna rna-seq
updated 11 months ago by 43k • written 13.9 years ago by 24k
298
votes
122
replies
32k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 7 months ago by ▴ 290 • written 13.7 years ago by 11k
36
votes
11
replies
32k
views
6 follow
Sjdboverhang Option In Star
updated 9 months ago by ▴ 90 • written 10.1 years ago by ★ 3.1k
78
votes
38
replies
32k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 6 weeks ago by ▴ 60 • written 7.8 years ago by 6.5k
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen RNA-Seq
updated 3 months ago by ▴ 60 • written 9.7 years ago by ▴ 90
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 5 months ago by 43k • written 14.0 years ago by ★ 1.7k
20
votes
9
replies
32k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart r bioconductor
updated 11 months ago by 87k • written 11.7 years ago by ▴ 120
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 8 months ago by • 0 • written 8.1 years ago by 20k
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline general
updated 6 months ago by 43k • written 14.1 years ago by 28k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 5 months ago by 43k • written 14.0 years ago by 161k
79
votes
86
replies
31k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 10 months ago by 43k • written 7.4 years ago by 20k
72
votes
71
replies
31k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 10 months ago by 43k • written 5.6 years ago by 87k
28
votes
16
replies
31k
views
11 follow
How Do I Convert From Bed Format To Gff Format?
gff galaxy bed
updated 6 months ago by 43k • written 14.6 years ago by 100k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 7 days ago by 22k • written 10.4 years ago by ★ 3.6k
14
votes
8
replies
31k
views
NarrowPeak format of ChiP-seq
ChIP-Seq tag-density
updated 10 months ago by • 0 • written 9.9 years ago by ▴ 210
4
votes
9
replies
30k
views
8 follow
How To Get Chromosome Position Given Rs Number?
snp chromosome position
updated 5 months ago by 141k • written 10.4 years ago by • 0
130
votes
19
replies
30k
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 11 weeks ago by 43k • written 4.6 years ago by ▴ 750
23
votes
12
replies
30k
views
9 follow
Extract Alignment From Very Large Bam File
bam
updated 11 weeks ago by 43k • written 11.9 years ago by ▴ 390
25
votes
11
replies
30k
views
9 follow
Bed For Agilent Sureselect All Exon Kits ?
bed exome agilent next-gen
written 11.4 years ago by 161k
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp amino-acids
updated 3 months ago by ▴ 80 • written 12.3 years ago by ▴ 110
52
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer annotation classification
updated 9 months ago by ★ 4.3k • written 10.7 years ago by ▴ 940
13
votes
3
replies
29k
views
What is the difference between blastx and tblastn?
assembly blast ncbi sequence
updated 10 months ago by 43k • written 4.8 years ago by ▴ 120
19
votes
9
replies
28k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis RNA-Seq ngs
updated 11 months ago by 43k • written 6.5 years ago by ▴ 510
1,000 results • Page 2 of 20
Recent Votes
Comment: Integration of transcriptomics and proteomics: difficult matching names
Comment: Integration of transcriptomics and proteomics: difficult matching names
A: How to filter mutant allele frequency in Variant Effect Predictor (VEP)?
Answer: Rename multiple fastq.gz files
Comment: VCF to human friendly form?
Comment: Integration of transcriptomics and proteomics: difficult matchin names
BRAKER3 genome annotation
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Recent Replies
Comment: Integration of transcriptomics and proteomics: difficult matching names by ntsopoul ▴ 60
you are right! Excel just did not find it...
Answer: Integration of transcriptomics and proteomics: difficult matching names by ntsopoul ▴ 60
I found a good solution but it is really cumbersome. I use UniProt.ws to derive unique gene names (readable names) and also ambiguous name…
Comment: Merging Outputs from plink --assoc and --hardy to Produce Table by Koketso • 0
Thank you so much. How about calculating allelic odds ratios? Which plink/R command can I use for that?
Comment: Integration of transcriptomics and proteomics: difficult matching names by ATpoint 81k
For such analysis I always first translate everything to Ensembl Gene IDs (biomaRt is a good help here) and then I do the matching with thi…
Comment: Rename multiple fastq.gz files by bk11 ★ 2.3k
Of course! If it worked, accept the answer.
Comment: Integration of transcriptomics and proteomics: difficult matching names by GenoMax 141k
I can see this in the list GI:2387631 Nup42 O Gene nucleoporin 42 10.72 5 24369961 24389011 + AA867018|AB067574|AI426644|AK077066|AK07…
Comment: Rename multiple fastq.gz files by Jérémie • 0
Sorry, I misunderstood. Thank you so much for this.
Comment: Integration of transcriptomics and proteomics: difficult matching names by sansan_96 ▴ 80
Hello, This conversion tool has been useful to me, maybe it can help you: https://biit.cs.ut.ee/gprofiler/convert
Comment: BRAKER3 genome annotation by sansan_96 ▴ 80
Perhaps eggNOG-MAPPER can be useful for functional annotation: 1. https://academic.oup.com/nar/article/47/D1/D309/5173662 2. http://eggnog…
Comment: BRAKER3 genome annotation by Buffo ★ 2.4k
I suggest searching for the difference between structural annotation (identifying the coordinates of the ORFs in a sequence) and functional…
Comment: Integration of transcriptomics and proteomics: difficult matchin names by ntsopoul ▴ 60
looks good but I cannot find either Nupl2 nor Nup42 in the list!
Comment: Integration of transcriptomics and proteomics: difficult matchin names by GenoMax 141k
This table from Jackson labs that correlates many mouse identifiers with external databases will help. Look at the headers of the columns t…
Comment: Rename multiple fastq.gz files by bk11 ★ 2.3k
I just gave hint in the comment above. Please try this, it should work for you. #!/bin/bash for file in `ls *fastq.gz`; do f…
Comment: BRAKER3 genome annotation by andorjkiss ▴ 40
I also have this exact same question. I have my entire genome annotated and a braker.GTF file, but without protein "product" names.
Answer: trouble using sequenceTubeMap in chromium installed on WSL by anovak ▴ 80
`Error: spawn vg ENOENT` means that Node could not find the `vg` command when it tried to run it. It got back [the `ENOENT` error code](htt…
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