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1,000 results • Page
5 of 20
Sort: Votes
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Views
Votes
Replies
8
votes
5
replies
3.6k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM
FASTQ
updated 16 months ago by
Ram
43k • written 8.9 years ago by
Andrew
▴ 60
8
votes
7
replies
1.5k
views
Splitting the overall RNA-seq data
RNA-Seq
6.9 years ago by
aeserrano
▴ 40
8
votes
10
replies
2.0k
views
FASTA of translated amino acid sequences in their six reading frames, which one is the optimal?
aminoacid
protein
peptide
Reading
optimal
frames
2.8 years ago by
Luis999
▴ 20
8
votes
7
replies
5.9k
views
Download human 3 UTR FASTA file
genome
8.2 years ago by
bharata1803
▴ 560
8
votes
8
replies
2.5k
views
6 follow
Blast Is Giving Me A Result Totally Unrelated To The Gene I Expect
blast
primer
updated 10.9 years ago by
Biostar
20 • written 11.0 years ago by
r.a.konrad
• 0
8
votes
30
replies
5.2k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.1 years ago by
wm
▴ 560 • written 4.1 years ago by
Researcher
▴ 20
8
votes
9
replies
1.5k
views
superimpose
discovery
ds
visualizer
2.9 years ago by
Alex
▴ 20
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 5.7 years ago by
Ram
43k • written 8.2 years ago by
Peng Huang
▴ 50
8
votes
20
replies
2.7k
views
Getting read depth for normal and tumour
R
WGS
vcf
5.1 years ago by
zizigolu
★ 4.3k
8
votes
5
replies
1.0k
views
Why could we infer a physical time scale (e.g. a billion year) from a phylogenetic analysis?
phylogeny
phylogenetic tree
4.5 years ago by
johnnytam100
▴ 110
8
votes
13
replies
1.7k
views
Mapped reads not mapping to a real sequence?
bam
sam
samtools
kallisto
14 months ago by
txema.heredia
▴ 110
8
votes
1
reply
1.2k
views
CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
CalculateGenotypePosteriors
gatk
trio
ped
3.3 years ago by
DareDevil
★ 4.3k
8
votes
5
replies
1.1k
views
Bioinformatics Definitions
genome
updated 2.9 years ago by
Dunois
★ 2.5k • written 2.9 years ago by
joe_genome
▴ 40
8
votes
11
replies
5.8k
views
RNASeq gender identification
RNA-Seq
6.7 years ago by
popayekid55
▴ 110
8
votes
25
replies
3.0k
views
construction of a database
sql
noSQL
neo4j
database
updated 13 months ago by
Ram
43k • written 3.0 years ago by
Debut
▴ 20
8
votes
6
replies
937
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari
structural-variants
r
vcf
venn-diagram
6 months ago by
Matteo Ungaro
▴ 100
8
votes
8
replies
2.8k
views
Making chain files
Assembly
genome
alignment
sequence
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
mc2548
▴ 50
8
votes
8
replies
1.9k
views
Sequence alignment algorithm for big size genes in MATLAB
alignment
Matlab
next-gen
7.0 years ago by
r.tor
▴ 50
8
votes
4
replies
2.4k
views
Global Sequence Alignment
alignment
11.0 years ago by
behrang
• 0
8
votes
11
replies
2.0k
views
using STAR instead of HISAT2
STAR
updated 21 months ago by
Ram
43k • written 21 months ago by
Chris
▴ 260
8
votes
3
replies
1.2k
views
Package installation error using Bioconda
antismash
Bioconda
17 months ago by
A_heath
▴ 160
8
votes
12
replies
3.4k
views
fastq file format error
fastq
illumina
updated 5.0 years ago by
Pierre Lindenbaum
161k • written 5.0 years ago by
hafiz.talhamalik
▴ 350
8
votes
11
replies
3.6k
views
Semantic Similarity selection in REVIGO: which is better? many clusters or few?
go
revigo
gene ontology
6.4 years ago by
Farbod
★ 3.4k
8
votes
7
replies
4.3k
views
ORF finder script
orf
open reading frame
bash
shell
sequencing
7.3 years ago by
ahm3dhany
▴ 20
8
votes
5
replies
2.0k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 7 months ago by
Ram
43k • written 2.6 years ago by
A_heath
▴ 160
8
votes
7
replies
3.9k
views
6 follow
Compatibility between my reference genome and GTF file
rna-seq
hisat2
alignment
reference genome
5.6 years ago by
Batu
▴ 250
8
votes
5
replies
3.1k
views
7 follow
What is the best way to merge multiple fasta files containing contigs?
Assembly
Anvi’o
fasta
updated 5.3 years ago by
zx8754
11k • written 5.3 years ago by
anastasia.gs17
• 0
8
votes
6
replies
2.3k
views
Using Bandage to finish ambiguous long-read assembly?
Assembly
Bandage
long reads
Unicycler
updated 5.2 years ago by
Biostar
20 • written 5.4 years ago by
predeus
★ 2.0k
8
votes
4
replies
865
views
Correlation network analysis
rna-seq
3.4 years ago by
Lepomis_8
▴ 30
8
votes
7
replies
1.3k
views
grep with -f switch is not working
grep
updated 4.4 years ago by
zx8754
11k • written 4.4 years ago by
3335098459
▴ 30
8
votes
5
replies
1.7k
views
differential expression analysis with DESeq2 & edgeR
RNA-Seq
3.5 years ago by
Rob
▴ 170
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf
VEP
11 months ago by
Jeremy Leipzig
22k
8
votes
6
replies
5.7k
views
miRanda output meaning?
rna-seq
updated 7.0 years ago by
WouterDeCoster
47k • written 7.0 years ago by
stijn.vandenbrande
▴ 40
8
votes
7
replies
4.1k
views
Error with Bowtie 2
bowtie2
alignment
6.9 years ago by
valerie
▴ 100
8
votes
8
replies
1.7k
views
6 follow
DESeq2 adjusted p-values of 0 when p-value > 0.05
RNA-seq
DEseq2
updated 3.0 years ago by
rodolfo.peacewalker
▴ 390 • written 3.0 years ago by
Adrian
• 0
8
votes
10
replies
758
views
bash script
whole-genome-sequencing
updated 19 days ago by
Ram
43k • written 26 days ago by
bestone
▴ 30
8
votes
5
replies
909
views
Why some genome assemblies don't have annotation?
genome
assembly
5.0 years ago by
860101959
▴ 10
8
votes
4
replies
2.0k
views
using different tools to identify differential exprssed genes
rna-seq
RNA-Seq
R
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Anushka
▴ 20
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq
differential expression
4.5 years ago by
guillaume.rbt
★ 1.0k
8
votes
6
replies
4.4k
views
Bwa Aln -Q 15 When To Use It? What Does It Do?
bwa
trimming
updated 11.8 years ago by
Istvan Albert
100k • written 11.8 years ago by
Kevin
▴ 640
8
votes
11
replies
1.9k
views
Sending files to Galaxy
Galaxy
fastq
7.6 years ago by
statfa
▴ 760
8
votes
14
replies
6.0k
views
Error in BWA-MEM running in linux
RNA-Seq
BWA-MEM
alignment
updated 6.0 years ago by
GenoMax
142k • written 6.0 years ago by
modarzi
▴ 170
8
votes
3
replies
5.3k
views
Bioinformatics project for a beginner
projects
updated 21 months ago by
Ram
43k • written 8.4 years ago by
dharshank.1096
▴ 30
8
votes
9
replies
3.0k
views
6 follow
Big difference in estimated duplicate reads between forward and reverse of paired-end RNA-seq
RNA-Seq
duplication
fastqc
updated 22 months ago by
rohitsatyam102
▴ 850 • written 4.5 years ago by
Eric Lim
★ 2.1k
8
votes
14
replies
2.4k
views
6 follow
Definition of "=" in comparing two genes
sequencing
gene
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
rdorey
• 0
8
votes
11
replies
2.7k
views
directionality of RRBS
directional
non-directional
RRBS
updated 2.8 years ago by
Papyrus
★ 2.9k • written 2.9 years ago by
basuanubhav
▴ 140
8
votes
20
replies
2.5k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 23 months ago by
Ram
43k • written 5.8 years ago by
Bara'a
▴ 270
8
votes
13
replies
2.4k
views
Issue about install Cutadapt in ubuntu1404
cutadapt
7.1 years ago by
Joe
▴ 30
8
votes
20
replies
3.0k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
6.3 years ago by
corend
▴ 70
8
votes
1
reply
8.6k
views
Correlation heatmaps: use correlation as clustering distance or not?
heatmap
RNA-Seq
clustering
5.0 years ago by
CuriousGuy
▴ 90
1,000 results • Page
5 of 20
Recent Votes
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
Answer: Design matrix Differential expression analysis
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Recent Replies
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 20
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 20
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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by
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82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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by
Ruqaiya
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This the tool still problematic?
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by
Ruqaiya
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Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
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by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
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