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Showing :
questions
1
vote
8
replies
968
views
Reads in IGV are mostly in intron regions
Patchseq
RNA-seq
10 months ago by
Kai_Qi
▴ 130
1
vote
1
reply
851
views
Software/packages for analyzing differential isoforms from RNA-seq data?
RNA-Seq
next-gen-sequencing
updated 21 months ago by
Ram
43k • written 3.4 years ago by
Kai_Qi
▴ 130
1
vote
4
replies
1.6k
views
Can't load reference sequence from file 'GRCh37.fa': Unexpected character 'M' found.
next-gen-sequencing
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 3.4 years ago by
Kai_Qi
▴ 130
2
votes
3
replies
1.0k
views
Get upstream and downstream exon's starting site and ending site of an retained introns
RNAseq
updated 2.8 years ago by
ATpoint
82k • written 2.9 years ago by
Kai_Qi
▴ 130
4
votes
5
replies
1.9k
views
how to understand the P value of the Deseq2 results
statistics
p_value
DEseq2
updated 3.0 years ago by
Michael Love
★ 2.6k • written 3.0 years ago by
Kai_Qi
▴ 130
8
votes
4
replies
2.6k
views
gzip: merged.fastq.gz not in gzip format
RNAseq
3.0 years ago by
Kai_Qi
▴ 130
2
votes
3
replies
1.0k
views
gencode gtf file derived geneID can't be annotated to gene symbol following Deseq2 manual
R
RNA-Seq
gene
3.1 years ago by
Kai_Qi
▴ 130
2
votes
3
replies
916
views
MEME cannot handle 318 sequence?
RNA-Seq
ChIP-Seq
rna-seq
genome
sequencing
updated 3.3 years ago by
Alex Reynolds
35k • written 3.3 years ago by
Kai_Qi
▴ 130
1
vote
1
reply
710
views
how to do GeneOntology in R using DAVID or other packages to recommed?
RNA-Seq
R
rna-seq
gene
3.3 years ago by
Kai_Qi
▴ 130
1
vote
1
reply
1.2k
views
Linear regression of the RNAseq results to get the genes whose expression change belong to the same trends
RNA-Seq
R
rna-seq
sequencing
updated 3.3 years ago by
thyleal
▴ 160 • written 3.3 years ago by
Kai_Qi
▴ 130
1
vote
3
replies
1.4k
views
Deseq2: time series in 1 condition. Error in nbinomLRT(object, full = full, reduced = reduced, quiet = quiet
R
RNA-Seq
next-gen
sequencing
3.3 years ago by
Kai_Qi
▴ 130
1
vote
3
replies
731
views
Removing ">" before coordinates and separate the coordinates in a single string format into a bed file
rna-seq
gene
next-gen
sequence
3.4 years ago by
Kai_Qi
▴ 130
2
votes
2
replies
577
views
Header of first sequence is missing after grep
rna-seq
RNA-Seq
sequencing
next-gen
gene
updated 3.4 years ago by
Pierre Lindenbaum
161k • written 3.4 years ago by
Kai_Qi
▴ 130
3
votes
4
replies
1.8k
views
ls: cannot access *.filter.trim.fastq.gz: No such file or directory (problems when combining individual steps into a full script)
RNA-Seq
rna-seq
sequencing
sequence
updated 3.4 years ago by
Ram
43k • written 3.4 years ago by
Kai_Qi
▴ 130
1
vote
6
replies
870
views
how to get the geneNames or bedfile from fasta sequences
RNA-Seq
genome
gene
ChIP-Seq
updated 3.4 years ago by
xiaoguang
▴ 140 • written 3.4 years ago by
Kai_Qi
▴ 130
0
votes
2
replies
1.5k
views
9th column of the GTF file is exon_id instead of gene_id, is this normal?
RNA-Seq
alignment
sequencing
3.4 years ago by
Kai_Qi
▴ 130
1
vote
3
replies
813
views
will the bam files mapped from Ensembl index be ok to do featurecount with mm10
RNA-Seq
rna-seq
alignment
sequence
3.4 years ago by
Kai_Qi
▴ 130
6
votes
2
replies
1.1k
views
samtools index cannot index concatenated bam?
alignment
rna-seq
RNA-Seq
next-gen
updated 3.4 years ago by
swbarnes2
14k • written 3.4 years ago by
Kai_Qi
▴ 130
0
votes
0
replies
596
views
How to visulize bed6 file generated from Pureclip analysis
RNA-Seq
rna-seq
sequencing
next-gen
3.4 years ago by
Kai_Qi
▴ 130
0
votes
1
reply
1.3k
views
using macs2 to call peaks on eCLIP-seq data
rna-seq
RNA-Seq
ChIP-Seq
3.4 years ago by
Kai_Qi
▴ 130
0
votes
0
replies
1.1k
views
Filtering uniquely mapping reads from bam files generated from STAR
rna-seq
RNA-Seq
ChIP-Seq
next-gen
3.4 years ago by
Kai_Qi
▴ 130
3
votes
7
replies
1.4k
views
intron/exon coordinates location: 5UTR/CDS/3UTR
RNA-Seq
rna-seq
sequencing
next-gen
updated 3.6 years ago by
Biostar
20 • written 3.8 years ago by
Kai_Qi
▴ 130
5
votes
11
replies
2.0k
views
sbacth on multiple fastq files sequentially
RNA-Seq
STAR
alignment
rna-seq
3.7 years ago by
Kai_Qi
▴ 130
3
votes
12
replies
2.2k
views
difficulties in merge multiple txt files from Rsubread feature counts to DESEQ2
R
RNA-Seq
rna-seq
DEseq2
3.7 years ago by
Kai_Qi
▴ 130
2
votes
2
replies
3.9k
views
error in hcluster although there is no NA/NAN/infinite
R
Heatmap
clustering
updated 3.8 years ago by
Jean-Karim Heriche
27k • written 3.8 years ago by
Kai_Qi
▴ 130
2
votes
1
reply
1.1k
views
MaxEntScan for mouse 5/3 splice site
RNA-Seq
genome
RNA-splice
MaxEntScan
3.8 years ago by
Kai_Qi
▴ 130
0
votes
0
replies
844
views
intersect between introns and the UTR/CDS bed files
genome
gtf
bed
gene
RNA-Seq
3.8 years ago by
Kai_Qi
▴ 130
0
votes
0
replies
785
views
Bedtools intersect gives empty files
rna-seq
sequencing
genome
gene
3.8 years ago by
Kai_Qi
▴ 130
0
votes
0
replies
647
views
comparison among the accumulation density curves
R
software error
3.8 years ago by
Kai_Qi
▴ 130
4
votes
1
reply
1.2k
views
Barplot labeling squeezed the bars
R
updated 3.8 years ago by
MatthewP
★ 1.4k • written 3.8 years ago by
Kai_Qi
▴ 130
2
votes
8
replies
667
views
make a vector containing several vectors in to a single one
R
3.8 years ago by
Kai_Qi
▴ 130
1
vote
5
replies
683
views
2 stages of GeneOntology in the same figure
R
next-gen
gene
updated 3.9 years ago by
jared.andrews07
★ 16k • written 3.9 years ago by
Kai_Qi
▴ 130
4
votes
9
replies
1.2k
views
barplot is missing in png file after saving
RNA-Seq
R
software error
next-gen
gene
updated 3.9 years ago by
Biostar
20 • written 3.9 years ago by
Kai_Qi
▴ 130
6
votes
13
replies
3.1k
views
How to modify my sbatch script to make it be able to be used for other files
RNA-Seq
next-gen
alignment
3.9 years ago by
Kai_Qi
▴ 130
6
votes
6
replies
896
views
Boxplot or ggplot
R
software error
RNA-Seq
sequencing
updated 3.9 years ago by
MatthewP
★ 1.4k • written 3.9 years ago by
Kai_Qi
▴ 130
1
vote
1
reply
2.1k
views
custom cluster or split heatmap?
R
software error
RNA-Seq
updated 3.9 years ago by
Ram
43k • written 3.9 years ago by
Kai_Qi
▴ 130
3
votes
3
replies
1.7k
views
error in reorder the bars of ggplots
RNA-Seq
R
rna-seq
software error
3.9 years ago by
Kai_Qi
▴ 130
4
votes
8
replies
2.0k
views
DESEQ2 on R cannot be installed on server
R
RNA-Seq
software error
rna-seq
sequencing
updated 4.0 years ago by
Ram
43k • written 4.0 years ago by
Kai_Qi
▴ 130
4
votes
11
replies
1.3k
views
using heat map to measure gene expression at different developmental stages
RNA-Seq
R
rna-seq
next-gen
4.0 years ago by
Kai_Qi
▴ 130
1
vote
3
replies
1.5k
views
How to use FIMO to find a motif among sequences?
RNA-Seq
rna-seq
software error
sequencing
updated 4.0 years ago by
Alex Reynolds
35k • written 4.0 years ago by
Kai_Qi
▴ 130
5
votes
16
replies
1.9k
views
MEME calling motifs from eCLIP-seq file generate no information
software-error
RNA-Seq
next-gen
ChIP-Seq
updated 10 months ago by
Ram
43k • written 4.0 years ago by
Kai_Qi
▴ 130
0
votes
0
replies
968
views
argument not recognizable cutadapt
RNA-Seq
software error
updated 4.0 years ago by
ATpoint
82k • written 4.0 years ago by
Kai_Qi
▴ 130
0
votes
1
reply
818
views
PureClip to analyze CLIP-SEQ
sequencing
RNA-Seq
updated 4.1 years ago by
GenoMax
141k • written 4.1 years ago by
Kai_Qi
▴ 130
2
votes
5
replies
1.1k
views
Packages in R for analyze premature stop codon and GC contents
R
RNA-Seq
updated 4.4 years ago by
Kristoffer Vitting-Seerup
★ 4.0k • written 4.4 years ago by
Kai_Qi
▴ 130
0
votes
0
replies
699
views
binomial test questions on determine the intron retention from reads on #E1I, #I and #IE2
RNA-Seq
R
4.5 years ago by
Kai_Qi
▴ 130
1
vote
7
replies
2.1k
views
Failed to install package(ASpli) in R
R
software error
RNA-Seq
4.5 years ago by
Kai_Qi
▴ 130
9
votes
20
replies
2.7k
views
Differential gene expression from 1 replicate using RPKM and edgeR
RNA-Seq
R
updated 4.6 years ago by
i.sudbery
19k • written 4.6 years ago by
Kai_Qi
▴ 130
1
vote
2
replies
1.7k
views
binomtest In R
R
RNA-Seq
4.6 years ago by
Kai_Qi
▴ 130
5
votes
4
replies
882
views
What does gene coordinates "CHR_MG117_PATCH:108783796-108806337"mean?
RNA-Seq
genome
updated 4.6 years ago by
GenoMax
141k • written 4.6 years ago by
Kai_Qi
▴ 130
6
votes
4
replies
3.3k
views
Get a bunch of ENTREZID into gene symbols
R
gene
RNA-Seq
updated 4.7 years ago by
piyushjo
▴ 700 • written 4.7 years ago by
Kai_Qi
▴ 130
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