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3
votes
9
replies
2.4k
views
ChIP-Seq Analysis allele specific way?
ChIP-Seq
ASE
MACS2
VCF
NGS
updated 3.6 years ago by
liang795
▴ 10 • written 5.2 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
1.2k
views
Does Nextera Transposase adapter sequence affects GATK HaplotypeCaller pipeline?
SNP
GATK
illumina
RNA-Seq
NGS
4.1 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
3.8k
views
Comment:
C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
4.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
3.8k
views
Comment:
C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
4.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
3.8k
views
Comment:
C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
4.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
3.8k
views
Comment:
C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
4.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
3.8k
views
Comment:
C: Split BAM file from paired end read into forward and reverse strand w.r.t refere
4.1 years ago by
Susmita Mandal
▴ 110
0
votes
10
replies
3.8k
views
Split BAM file from paired end read into forward and reverse strand w.r.t reference genome
RNA-Seq
NGS
SNP
Variant Calling
samtools
updated 4.1 years ago by
ATpoint
81k • written 4.1 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
28k
views
Comment:
C: SAM flags meaning
4.1 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
507
views
Tools and/or methods to detect allelic mapping bias.
RNA-Seq
SNP
variant calling
ngs
alelle specific
4.2 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
1.2k
views
Comment:
C: Making pattern of GT:AD:DP:PL column values to be replaced by o and 1.
4.2 years ago by
Susmita Mandal
▴ 110
1
vote
1
reply
2.4k
views
Comment:
C: ChIP-Seq Analysis allele specific way?
4.2 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
1.8k
views
Comment:
C: Splitting BAM file from paired end into forward and reverse strands?
4.2 years ago by
Susmita Mandal
▴ 110
0
votes
2
replies
1.8k
views
Splitting BAM file from paired end into forward and reverse strands?
RNA-Seq
samtools
ngs
rna-seq
VCF
4.2 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
8.6k
views
Comment:
C: Tools For Analysis Allele Specific Expression In Rna-Seq Data?
4.3 years ago by
Susmita Mandal
▴ 110
1
vote
1
reply
4.3k
views
Comment:
C: Allele Specific Expression Analysis
4.3 years ago by
Susmita Mandal
▴ 110
3
votes
10
replies
4.3k
views
Allele Specific Expression Analysis
SNP
Allele specific
RNA-Seq
X chromosome
STAR
updated 4.3 years ago by
ta_awwad
▴ 340 • written 5.5 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
2.9k
views
Comment:
C: scRNA-seq gene expression gradient onto tSNE plot
4.5 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
2.7k
views
Comment:
C: STAR genome genrate taking long time and less thread.
4.7 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
4.3k
views
Comment:
C: Allele Specific Expression Analysis
4.8 years ago by
Susmita Mandal
▴ 110
1
vote
2
replies
1.4k
views
Outliers in a boxplot: Necessary or not?
RNA-Seq
Statistics
R
4.8 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
1.4k
views
Comment:
C: Moving average plot of gene expression ratio along the chromosome length
4.9 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
1.4k
views
Comment:
C: Moving average plot of gene expression ratio along the chromosome length
4.9 years ago by
Susmita Mandal
▴ 110
0
votes
4
replies
1.4k
views
Moving average plot of gene expression ratio along the chromosome length
RNA-Seq
R
Bioconductor
gene
next-gen
4.9 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
3.0k
views
Comment:
C: Convert RefseqID to EntrezID
4.9 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
3.0k
views
Comment:
A: Convert RefseqID to EntrezID
4.9 years ago by
Susmita Mandal
▴ 110
1
vote
0
replies
957
views
Comment:
C: Getting only Indels and no SNPs after variant calling variant calling using Hapl
4.9 years ago by
Susmita Mandal
▴ 110
1
vote
1
reply
1.7k
views
Comment:
C: Allele specific expression analysis using human cell line
4.9 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
957
views
Comment:
C: Getting only Indels and no SNPs after variant calling variant calling using Hapl
4.9 years ago by
Susmita Mandal
▴ 110
3
votes
4
replies
957
views
Getting only Indels and no SNPs after variant calling variant calling using HaplotypeCaller
RNA-Seq
BAM
SNP
GATK
Variant Calling
4.9 years ago by
Susmita Mandal
▴ 110
1
vote
0
replies
880
views
Is it advisable to do allele specific expression analysis on single cell RNA-Seq data?
RNA-Seq
Single-cell
NGS
ASE
SNP
updated 5.0 years ago by
Biostar
20 • written 5.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
1.7k
views
Comment:
C: Allele specific expression analysis using human cell line
5.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
1.7k
views
Comment:
C: Allele specific expression analysis using human cell line
5.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
1.7k
views
Comment:
C: Allele specific expression analysis using human cell line
5.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
1.7k
views
Comment:
C: Allele specific expression analysis using human cell line
5.1 years ago by
Susmita Mandal
▴ 110
4
votes
12
replies
1.7k
views
Allele specific expression analysis using human cell line
RNA-Seq
ASE
NGS
SNP
Affimetrix
updated 5.1 years ago by
nsmi8446
▴ 170 • written 5.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
6.1k
views
Comment:
C: Converting Microarray SNP data into VCF format
5.1 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
6.1k
views
Comment:
C: Converting Microarray SNP data into VCF format
5.1 years ago by
Susmita Mandal
▴ 110
0
votes
2
replies
6.1k
views
Comment:
C: Converting Microarray SNP data into VCF format
5.1 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
679
views
Genome Annotations? RepeatMasker class/family? Regulation?
RNA-Seq
RepeatMasker
Annotation
NGS
5.1 years ago by
Susmita Mandal
▴ 110
0
votes
2
replies
2.0k
views
ChIP-Seq density plot of the TSS regions?
ChIP-Seq
Deeptools
Bedtools
IGV
ASE
updated 5.1 years ago by
i.sudbery
18k • written 5.1 years ago by
Susmita Mandal
▴ 110
2
votes
2
replies
10k
views
How to include genes having negative fold change in the log2 FC plot?
RNA-Seq
log2
NGS
fold change
ASE
updated 5.2 years ago by
swbarnes2
14k • written 5.2 years ago by
Susmita Mandal
▴ 110
0
votes
0
replies
2.4k
views
Comment:
C: ChIP-Seq Analysis allele specific way?
5.2 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
2.4k
views
Comment:
C: ChIP-Seq Analysis allele specific way?
5.2 years ago by
Susmita Mandal
▴ 110
10
votes
13
replies
9.9k
views
8 follow
What is RPKM/FPKM > 1 or 3 or 5?
RNA-Seq
rpkm
fpkm
normalization
ngs
updated 23 months ago by
ccfpwll
• 0 • written 5.2 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
9.9k
views
Comment:
C: What is RPKM/FPKM > 1 or 3 or 5?
5.2 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
9.9k
views
Comment:
C: What is RPKM/FPKM > 1 or 3 or 5?
5.2 years ago by
Susmita Mandal
▴ 110
0
votes
2
replies
9.9k
views
Comment:
C: What is RPKM/FPKM > 1 or 3 or 5?
5.2 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
6.1k
views
Comment:
C: Converting Microarray SNP data into VCF format
5.3 years ago by
Susmita Mandal
▴ 110
0
votes
1
reply
6.1k
views
Comment:
C: Converting Microarray SNP data into VCF format
5.3 years ago by
Susmita Mandal
▴ 110
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