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1,000 results • Page
5 of 20
Sort: Views
Rank
Views
Votes
Replies
79
votes
16
replies
48k
views
11 follow
How do you cite a tool that doesn't have a publication?
citation
academic
style
updated 8.0 years ago by
Emily
23k • written 8.1 years ago by
novice
★ 1.1k
30
votes
10
replies
48k
views
Filtering A Sam File For Quality Scores
sam
updated 12.0 years ago by
Sukhi Singh
11k • written 12.0 years ago by
Varun Gupta
★ 1.3k
39
votes
14
replies
48k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl
fasta
python
parsing
updated 24 months ago by
Michael
54k • written 12.3 years ago by
Mohammad Reza Bakhtiarizadeh
▴ 350
3
votes
5
replies
48k
views
Convert text file to VCF file ?
vcf
updated 10 months ago by
Ram
43k • written 9.1 years ago by
CrazyB
▴ 280
24
votes
14
replies
47k
views
7 follow
Gene symbol convert to Entrez ID
Entrez
R
biomart
updated 5.6 years ago by
zx8754
11k • written 6.9 years ago by
landscape95
▴ 190
32
votes
8
replies
47k
views
7 follow
Difference Between "Pipeline" And "Workflow" ?
next-gen
sequencing
written 12.2 years ago by
Pascal
★ 1.5k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 9 months ago by
Ram
43k • written 10.9 years ago by
hicsuntdrac0nis
▴ 250
6
votes
12
replies
47k
views
9 follow
Opening A Fasta File In Windows
fasta
blast
makeblastdb
updated 12.1 years ago by
Vivek
• 0 • written 12.1 years ago by
Vivek
• 0
49
votes
4
replies
47k
views
How To Convert The Bed File To Ped File
bed
ped
updated 19 months ago by
sonsunjirachote
• 0 • written 13.7 years ago by
Austinlew
▴ 310
22
votes
4
replies
47k
views
Convert plink files to VCF: Reference allele file
SNP
genome
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Ishtiaq Ahmad Khan
▴ 70
112
votes
24
replies
47k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp
samtools
alignment
next-gen
sequencing
updated 19 months ago by
Ram
43k • written 12.9 years ago by
Matthieu
▴ 480
118
votes
74
replies
46k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 17 months ago by
GenoMax
141k • written 13.4 years ago by
Casbon
★ 3.3k
77
votes
18
replies
46k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 20 months ago by
Dan
• 0 • written 13.9 years ago by
Science_Robot
★ 1.1k
57
votes
23
replies
46k
views
14 follow
Bam File: Change Chromosome Notation
samtools
bam
updated 2.9 years ago by
zx8754
11k • written 12.5 years ago by
Lisanne
▴ 160
117
votes
66
replies
46k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 13 months ago by
Ram
43k • written 5.8 years ago by
ATpoint
81k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 11 days ago by
psb7
▴ 20 • written 5.6 years ago by
Kevin Blighe
87k
17
votes
5
replies
46k
views
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
heatmap
r
updated 12.4 years ago by
Michael
54k • written 12.4 years ago by
C Shao
▴ 140
11
votes
8
replies
45k
views
Converting Smiles To Iupac Chemical Name?
updated 11.8 years ago by
Egon Willighagen
5.4k • written 11.8 years ago by
dimkal
▴ 730
9
votes
12
replies
45k
views
8 follow
Tools to view fastq file
fastq
updated 9 months ago by
Ram
43k • written 8.0 years ago by
Roden Luo
▴ 40
81
votes
6
replies
45k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam
samtools
next-gen
updated 2.1 years ago by
Ram
43k • written 12.0 years ago by
Stefano Berri
4.4k
49
votes
10
replies
45k
views
When and why is bwa aln better then bwa mem?
aln
comparison
bwa
mem
updated 3.0 years ago by
Ram
43k • written 9.5 years ago by
dariober
14k
298
votes
27
replies
45k
views
33 follow
Forum:
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq
sequencing
papers
updated 21 months ago by
Ram
43k • written 8.2 years ago by
CandiceChuDVM
★ 2.4k
32
votes
7
replies
45k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq
deseq2
tpm
updated 21 months ago by
Ram
43k • written 9.1 years ago by
Tom Harrop
▴ 170
22
votes
7
replies
45k
views
Extracting cells only from one condition (Seurat)
single cell rnaseq
seurat
RNA-Seq
R
updated 3.0 years ago by
Tatyana
▴ 50 • written 4.2 years ago by
V
▴ 380
30
votes
14
replies
45k
views
9 follow
Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
rna-seq
differential
expression
updated 7.9 years ago by
Biostar
20 • written 11.9 years ago by
Sahel
▴ 310
34
votes
11
replies
44k
views
8 follow
Where Can I Download Some Bam Files?
bam
RNA-seq
updated 3 months ago by
Ram
43k • written 11.9 years ago by
snakesgun
▴ 160
32
votes
11
replies
44k
views
9 follow
How To Sort Sam File
samtools
sam
updated 15 months ago by
Ram
43k • written 10.2 years ago by
Chen Sun
★ 1.1k
134
votes
27
replies
44k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.0 years ago by
Ram
43k • written 12.0 years ago by
lh3
33k
25
votes
23
replies
44k
views
12 follow
How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
samtools
next-gen
sequencing
fasta
updated 10.2 years ago by
mobiusklein
▴ 180 • written 13.9 years ago by
Casey Bergman
18k
17
votes
3
replies
44k
views
What'S The Meaning Of "Bridge Pcr" In The Next Generation Sequencing
pcr
sequencing
updated 10.8 years ago by
William
★ 5.3k • written 10.8 years ago by
weiqiangduan
▴ 130
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 23 months ago by
Ram
43k • written 9.1 years ago by
MAPK
★ 2.1k
63
votes
8
replies
44k
views
6 follow
Why Do You Need To Use Cdna For Rna-Seq?
rna-seq
cdna
updated 7.7 years ago by
SeqFreak
• 0 • written 11.5 years ago by
Justin
▴ 460
23
votes
8
replies
44k
views
Convert .Txt File To Bed File
bed
updated 9.8 years ago by
inesdesantiago
▴ 260 • written 12.6 years ago by
Bioscientist
★ 1.7k
32
votes
10
replies
44k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat
illumina
strand
updated 18 months ago by
Ram
43k • written 11.2 years ago by
Nicolas Rosewick
10k
25
votes
9
replies
44k
views
Converting Gff To Bed With Bedtools?
gff
bed
bedtools
updated 10 weeks ago by
Ram
43k • written 11.3 years ago by
user
▴ 940
112
votes
56
replies
44k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq
next-gen
sequencing
fusion
updated 19 months ago by
Ram
43k • written 11.9 years ago by
KS
▴ 380
32
votes
5
replies
44k
views
What is Differential Expression?
DNA
genes
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
LoveLeh
▴ 50
85
votes
19
replies
44k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly
quality
next-gen
updated 2.2 years ago by
WANG
▴ 10 • written 11.2 years ago by
diltsjeri
▴ 470
3
votes
5
replies
44k
views
how to set the size of cell of heatmap.2 in R
heatmap.2
R
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
Zhilong Jia
★ 2.2k
53
votes
19
replies
43k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 14 months ago by
Ram
43k • written 12.0 years ago by
Sukhi Singh
11k
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 14 months ago by
Ram
43k • written 9.0 years ago by
MAPK
★ 2.1k
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
ashotmarg2004
▴ 130 • written 7.8 years ago by
William
★ 5.3k
37
votes
15
replies
43k
views
8 follow
FPKM vs raw counts vs RPKM
counts
rpkm
raw
fpkm
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
NHEJ
▴ 360
26
votes
9
replies
43k
views
How Logfc Value Is Calculated In Edger?
edger
r
RNA-seq
updated 13 months ago by
Ram
43k • written 10.6 years ago by
nbvasani
▴ 240
60
votes
52
replies
43k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 13 months ago by
Ram
43k • written 7.6 years ago by
steve
★ 3.5k
48
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 11 weeks ago by
Picasa
▴ 640 • written 7.5 years ago by
ZheFrench
▴ 570
14
votes
6
replies
43k
views
Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
ncbi
updated 10.7 years ago by
SRKR
▴ 180 • written 10.7 years ago by
bioinfo
▴ 830
121
votes
35
replies
43k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 11 months ago by
Ram
43k • written 6.8 years ago by
ropolocan
▴ 810
25
votes
6
replies
43k
views
Aggregate multiple rows based on common values in given columns
R
updated 5.6 years ago by
zx8754
11k • written 8.4 years ago by
writersblog02
▴ 70
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 12 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
1,000 results • Page
5 of 20
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The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
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141k
I don't think MEGA supports GPU's: https://www.megasoftware.net/web_help_11/Part_I_Getting_Started/Installing_MEGA/System_Requirements.htm
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
ATpoint
81k
You can, if you use RStudio via Docker, for example `bioconductor/bioconductor_docker`. I currently manage many different projects with thi…
Comment: bam merging for archaic samples
by
Matteo Ungaro
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@Pierre Lindenbaum I see. So, I can actually manipulate just one single RG tag at the time with `samtools`? Which flag should I use, or sho…
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RG tag "L9302" is missing the the BAM header. You should have something like this in the BAM header ``` @RG ID:L9302 SM:L9302 ``` may be…
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161k
> . Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to? samtools depth i…
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Hello Franco. I am very much new with bioinformatics but I have been tasked with studying the radius of gyration of a timeseries of a prote…
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That makes a lot more sense. Thank you.
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Type ``` help("read.idat") ``` and read the example at the bottom of the page, which shows you how to set the `other$Detection` component o…
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Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely
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14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
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by
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81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file
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14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
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Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
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Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
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