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questions
0
votes
0
replies
180
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
4 weeks ago by
Apex92
▴ 280
0
votes
1
reply
173
views
How to perform enrichment p-value for a motif
Enrichment
statistics
updated 6 weeks ago by
Trivas
★ 1.7k • written 6 weeks ago by
Apex92
▴ 280
0
votes
0
replies
144
views
How to calculate the percentage of hydrophobic amino acids?
genome
RNA-Seq
Splicing
sequencing
8 weeks ago by
Apex92
▴ 280
0
votes
12
replies
2.4k
views
Differential gene expression analysis with no replicates using edgeR
edgeR
RNA-seq
DEG
updated 4 months ago by
Sajad
▴ 90 • written 16 months ago by
Apex92
▴ 280
0
votes
1
reply
449
views
How to interpret the negative Log2FC from DESeq2 output?
DESeq2
statistics
gene-expression
DEG
updated 6 months ago by
Ram
43k • written 6 months ago by
Apex92
▴ 280
0
votes
18
replies
1.8k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 8 months ago by
GenoMax
141k • written 8 months ago by
Apex92
▴ 280
0
votes
2
replies
411
views
Is chi-square test suitable for my categorical data?
statistics
r
8 months ago by
Apex92
▴ 280
0
votes
2
replies
479
views
Testing Gene Set Overlap with Binomial Distribution or Hypergeometric Distribution
statistics
Enrichment
8 months ago by
Apex92
▴ 280
0
votes
1
reply
433
views
How to run quantifier from miRDeep2 (miRNA seqs from MirGeneDB)
quantifier
alignment
mapping
mirdeep2
7 months ago by
Apex92
▴ 280
0
votes
0
replies
409
views
Finding ORF via UCSC genome browser
genome
RNA-Seq
sequencing
10 months ago by
Apex92
▴ 280
0
votes
2
replies
589
views
Confirming intron length
genome
RNA-Seq
sequencing
10 months ago by
Apex92
▴ 280
0
votes
0
replies
463
views
How the "IJC" is calculated in rMATS tool?
Sashimi
sequencing
alignment
rMATS
rna-seq
11 months ago by
Apex92
▴ 280
1
vote
2
replies
608
views
How to split a fastq file to multiples fastq files
fastq
sequencing
rna-seq
12 months ago by
Apex92
▴ 280
4
votes
7
replies
1.1k
views
How to demultiplex single-end dual indexed run - NextSeq 500
sequencing
bcl2fastq
rna-seq
13 months ago by
Apex92
▴ 280
0
votes
5
replies
944
views
How to get human cDNA sequences together with UTR regions?
transcripts
cDNA
genome
rna-seq
updated 13 months ago by
Istvan Albert
100k • written 13 months ago by
Apex92
▴ 280
2
votes
2
replies
626
views
How to compare different illumina indices with each other to see how similar or different they are
alignment
sequencing
rna-seq
updated 14 months ago by
GenoMax
141k • written 14 months ago by
Apex92
▴ 280
1
vote
6
replies
1.1k
views
Bowtie error when indexing a reference file
bowtie
RNA-seq
updated 15 months ago by
ATpoint
82k • written 15 months ago by
Apex92
▴ 280
4
votes
2
replies
1.6k
views
How to download the entire Run from Illumina BaseSpace
illumina
sequencing
RNA-seq
17 months ago by
Apex92
▴ 280
2
votes
3
replies
1.4k
views
How to open/work with wig or tdf files
IGV
sequencing
wig
rna-seq
tdf
17 months ago by
Apex92
▴ 280
2
votes
3
replies
734
views
The concept of differentially expressed genes at exon and intron level
transcription
DEG
RNA-Seq
sequencing
genome
updated 20 months ago by
lieven.sterck
15k • written 20 months ago by
Apex92
▴ 280
3
votes
3
replies
1.0k
views
How to choose one TSS for every gene using Gencode annotation file?
TSS
transcription
sequencing
RNA-seq
20 months ago by
Apex92
▴ 280
1
vote
2
replies
869
views
Cell cycle arrest analysis using bulk RNA-seq
rna-seq
RNA-Seq
sequencing
cell-cycle
genome
20 months ago by
Apex92
▴ 280
0
votes
0
replies
320
views
How robust is rMATS when swapping samples?
splicing
rmats
RNA-seq
STAR
alternative
21 months ago by
Apex92
▴ 280
4
votes
2
replies
849
views
Error when using edgeR with only two samples
RNA-seq
DGE
sequencing
edgeR
22 months ago by
Apex92
▴ 280
2
votes
4
replies
779
views
How to perform differential gene expression analysis with only one replicate in each condition
RNA-seq
DEG
DESeq2
sequencing
updated 23 months ago by
Michael
54k • written 23 months ago by
Apex92
▴ 280
0
votes
0
replies
607
views
How to edit a SAM file using pysam
sam
pysam
mapping
algnment
bam
2.1 years ago by
Apex92
▴ 280
0
votes
5
replies
1.0k
views
What could be a good balance between baseMean and Log2FoldChange?
expression
gene
statistics
DESeq2
DEG
2.1 years ago by
Apex92
▴ 280
3
votes
2
replies
546
views
What is a suitable Gene Ontology Enrichment Analaysis tool?
statistics
Enrichment
Ontology
2.1 years ago by
Apex92
▴ 280
0
votes
0
replies
557
views
What is the latest and reliable Gene Ontology analysis tool in Python
sequencing
ontology
genome
enrichr
RNA-Seq
2.1 years ago by
Apex92
▴ 280
0
votes
4
replies
2.5k
views
NextSeq 2000 bcl2fastq conversion
sequencing
bcl2fastq
fastq
updated 2.1 years ago by
GenoMax
141k • written 2.1 years ago by
Apex92
▴ 280
0
votes
2
replies
1.7k
views
bcl2fastq error with RunInfo.xml
sequencing
bcl2fastq
fastq
updated 12 months ago by
Janki
• 0 • written 2.1 years ago by
Apex92
▴ 280
2
votes
4
replies
867
views
How to get rid of mis-assigned reads without having bcl files or index information?
alignment
fastq
RNA-seq
updated 2.2 years ago by
swbarnes2
14k • written 2.2 years ago by
Apex92
▴ 280
6
votes
7
replies
1.6k
views
Analyzing and slicing FASTQ file entries using Python
biopython
sequence
performance
FASTQ
updated 2.2 years ago by
Pierre Lindenbaum
161k • written 2.2 years ago by
Apex92
▴ 280
1
vote
3
replies
996
views
How to output FASTQ file with four lines per sequence?
biopython
python
fastq
updated 2.2 years ago by
cpad0112
21k • written 2.2 years ago by
Apex92
▴ 280
1
vote
3
replies
702
views
How many skipped exons is expected by chance?
splicing
statistics
exon
rna-seq
updated 2.2 years ago by
Istvan Albert
100k • written 2.2 years ago by
Apex92
▴ 280
2
votes
3
replies
911
views
Any tool to detect differential splicing of a gene between samples?
sequence
MISO
splicing
bam
RNA-Seq
2.2 years ago by
Apex92
▴ 280
0
votes
3
replies
1.3k
views
How to interpret arcs in the Sashimi plots (IGV)?
sequencing
Sashimi
IGV
alignment
rna-seq
updated 2.2 years ago by
German.M.Demidov
★ 2.9k • written 2.2 years ago by
Apex92
▴ 280
2
votes
7
replies
1.6k
views
Why there are symmetric splice junctions on IGV?
sequencing
bam
IGV
alignment
rna-seq
2.2 years ago by
Apex92
▴ 280
0
votes
0
replies
520
views
Segemehl -D option doesnt work for allowing differences
alignment
RNA-Seq
segemehl
updated 2.6 years ago by
Ram
43k • written 2.6 years ago by
Apex92
▴ 280
1
vote
2
replies
2.2k
views
How to calculate probability of overlap between two sets
overlap
r
statistics
updated 2.6 years ago by
Istvan Albert
100k • written 2.6 years ago by
Apex92
▴ 280
3
votes
4
replies
2.3k
views
the --fraction option of featureCounts
RNA-Seq
featureCounts
rna-seq
genome
sequencing
2.7 years ago by
Apex92
▴ 280
0
votes
0
replies
453
views
How to divide reads mapping to two different genes using featureCounts
featureCounts
mapping
alignment
rna-seq
2.8 years ago by
Apex92
▴ 280
2
votes
6
replies
2.4k
views
How to find overlapping coordinates of a gtf file
gtf-file
sequencing
genome
annotation
RNA-Seq
updated 2.8 years ago by
Alex Reynolds
35k • written 2.8 years ago by
Apex92
▴ 280
0
votes
1
reply
499
views
RefSeq obtained from genome.ucsc.edu
Genome-browser
Annotation
sequence
updated 13 months ago by
Ram
43k • written 3.0 years ago by
Apex92
▴ 280
1
vote
2
replies
816
views
How to get Python code to run correctly for hetero-dimerization analysis
python
sequence
programming
FASTA
updated 3.0 years ago by
cpad0112
21k • written 3.0 years ago by
Apex92
▴ 280
0
votes
2
replies
783
views
Hetero-dimerization analysis with two FASTA files
sequence
FASTA
python
awk
bash
updated 3.0 years ago by
Ram
43k • written 3.0 years ago by
Apex92
▴ 280
2
votes
21
replies
3.1k
views
How to loop on two fasta files for hetero-dimerization analysis
fasta
script
python
sequence
updated 3.0 years ago by
cpad0112
21k • written 3.0 years ago by
Apex92
▴ 280
3
votes
3
replies
1.2k
views
how to intersect two files based on three columns
python
awk
bash
updated 3.0 years ago by
5heikki
11k • written 3.1 years ago by
Apex92
▴ 280
13
votes
10
replies
2.3k
views
6 follow
How to reverse the order of **records** in a fasta file
sequence
pipeline
programming
fasta
updated 3.0 years ago by
cpad0112
21k • written 3.1 years ago by
Apex92
▴ 280
10
votes
18
replies
3.3k
views
How to concatenate FASTA files in a specific order based on sequence ID
sequence
fasta
awk
python
pipeline
3.1 years ago by
Apex92
▴ 280
66 results • Page
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