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questions
0
votes
0
replies
225
views
find_marker_genes throws error using case_groups and control_groups
stereopy
python
find_marker_genes
6 months ago by
Chirag Nepal
★ 2.4k
5
votes
4
replies
2.8k
views
Predict if the mutation is activating or deactivating
SNV INDEL
Activating
Deactivating mutations
updated 3.3 years ago by
Biostar
20 • written 7.6 years ago by
Chirag Nepal
★ 2.4k
4
votes
2
replies
1.4k
views
Mapping variable read length
alignment
updated 3.6 years ago by
Biostar
20 • written 6.2 years ago by
Chirag Nepal
★ 2.4k
0
votes
3
replies
1.0k
views
Find HBV integration sites in human genome.
ChimericReads
HumanVirusGenome
CAGE-seq
updated 4.1 years ago by
Pierre Lindenbaum
161k • written 4.1 years ago by
Chirag Nepal
★ 2.4k
1
vote
2
replies
729
views
Mapping reads on ENCODEBlackListedRegion
CAGE-seq
ENCODEBlackListedRegion
4.1 years ago by
Chirag Nepal
★ 2.4k
1
vote
4
replies
1.5k
views
Visualize paired end reads
RNA-Seq
Paired-end
alignment
updated 4.2 years ago by
jbalberge
▴ 170 • written 4.2 years ago by
Chirag Nepal
★ 2.4k
0
votes
5
replies
2.4k
views
Position of SNPs with respect to codon
Codon
SNP
tRNA
updated 21 months ago by
Ram
43k • written 8.4 years ago by
Chirag Nepal
★ 2.4k
0
votes
0
replies
1.1k
views
Virmid mutation calling, error
Virmid
Mutation
updated 5.7 years ago by
Ram
43k • written 6.2 years ago by
Chirag Nepal
★ 2.4k
1
vote
1
reply
1.6k
views
KEGG pathway file for running genome music path-scan
MuSic
KEGG
5.9 years ago by
Chirag Nepal
★ 2.4k
0
votes
2
replies
2.1k
views
Determine whether it is MSI (micro satellite instability) or not
MSI
msisensors
updated 5.9 years ago by
lvulliard
▴ 60 • written 5.9 years ago by
Chirag Nepal
★ 2.4k
1
vote
1
reply
1.7k
views
Count intron retention reads from BAM files
samtools
intron-retention
updated 6.1 years ago by
d-cameron
★ 2.9k • written 6.1 years ago by
Chirag Nepal
★ 2.4k
7
votes
4
replies
6.4k
views
Best/right way to quantify small RNA transcripts
small RNA-seq
RPM
multi-mapping
updated 11 months ago by
Sergio
• 0 • written 6.2 years ago by
Chirag Nepal
★ 2.4k
7
votes
6
replies
11k
views
How To Extract Spliced Rnaseq Reads
RNA-seq
updated 16 months ago by
Ram
43k • written 10.3 years ago by
Chirag Nepal
★ 2.4k
0
votes
1
reply
1.4k
views
Transcriptional strand bias on SNV from exome data
SNV
exome
Strand-bias
updated 6.7 years ago by
Biostar
20 • written 6.7 years ago by
Chirag Nepal
★ 2.4k
4
votes
7
replies
2.2k
views
Mismatch on first base gives wrong TSS
first-base mismatch
clip-mismatch
CIGAR
CAGE
updated 7.0 years ago by
Charles Plessy
★ 2.9k • written 7.2 years ago by
Chirag Nepal
★ 2.4k
4
votes
3
replies
2.4k
views
Exome-seq; Which tools to predict significantly muated genes .
music
varscan
CNV
updated 7.4 years ago by
Biostar
20 • written 7.5 years ago by
Chirag Nepal
★ 2.4k
1
vote
3
replies
2.1k
views
Transcriptional regulator genes list
Genelist
Transcriptional-regulator
updated 7.5 years ago by
ZhouK.R.
▴ 10 • written 8.1 years ago by
Chirag Nepal
★ 2.4k
0
votes
1
reply
1.4k
views
Histone modifications data on embryonic stem cells to differentiated stages
ESC
H3K4me1
H3K4me3
7.6 years ago by
Chirag Nepal
★ 2.4k
2
votes
0
replies
1.6k
views
4C/5C Interaction Data from RoadMap
Long range interaction
4c
5C
HiC
7.7 years ago by
Chirag Nepal
★ 2.4k
2
votes
3
replies
1.5k
views
Genome Music: Most significant hits lack p-value
Genome Music
p-value
updated 8.0 years ago by
Chris Miller
22k • written 8.0 years ago by
Chirag Nepal
★ 2.4k
1
vote
2
replies
2.4k
views
Pathway enrichment for Copy Number Alterations (CNA)
Genome-Music
CNV
CNA
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Chirag Nepal
★ 2.4k
0
votes
0
replies
1.9k
views
Histone Chip-seq (H3K4me3) data from normal/tumor pair.
Tumor-Normal
ChIP-Seq
H3K4me3
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Chirag Nepal
★ 2.4k
1
vote
0
replies
2.8k
views
Identify list of reoccurring genes from CNV using GISTIC
CNV
GISTIC
copy-number
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Chirag Nepal
★ 2.4k
2
votes
2
replies
2.4k
views
genome music bmr calc-covg [Run in parallel]
coverage
music
updated 20 months ago by
Ram
43k • written 8.5 years ago by
Chirag Nepal
★ 2.4k
2
votes
2
replies
2.2k
views
Cancer signature, Transition/Transversion inclduing tri-nucleotide
cosmic-signature
SNP
transition-transversion
exome
updated 20 months ago by
Ram
43k • written 8.5 years ago by
Chirag Nepal
★ 2.4k
1
vote
5
replies
1.9k
views
JISTIC. Make Probe location file to compare copy number among samples
DNAcopy
copyNumber
JISTIC
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Chirag Nepal
★ 2.4k
3
votes
1
reply
3.5k
views
varscan2: merge the CNA segments using mergeSegments.pl
CNV
mergeSegments.pl
varscan
updated 18 months ago by
Ram
43k • written 8.7 years ago by
Chirag Nepal
★ 2.4k
0
votes
2
replies
1.4k
views
Non-synonomous mutations fall on CDS and (Intron/UTR) due to alternative transcripts of same gene
polyphen
SNP
annovar
updated 18 months ago by
Ram
43k • written 8.7 years ago by
Chirag Nepal
★ 2.4k
32
votes
15
replies
27k
views
GATK, SAM file doesn't have any read groups defined in the header
SAM
GATK
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Chirag Nepal
★ 2.4k
2
votes
1
reply
1.5k
views
Multiple SNPs within few bases
somaticSniper
SNP
varscan
updated 17 months ago by
Ram
43k • written 8.8 years ago by
Chirag Nepal
★ 2.4k
0
votes
1
reply
1.6k
views
Random selection of genes from another pool of genes, with similar expression level
expression-level
random-selection
updated 23 months ago by
Ram
43k • written 9.1 years ago by
Chirag Nepal
★ 2.4k
2
votes
8
replies
4.6k
views
Annotate RNA-seq transcripts to transcript class as NMD (nonsense mediated decay)
transcripts
nonsense-mediated-decay
rna-seq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Chirag Nepal
★ 2.4k
1
vote
3
replies
2.5k
views
count reference and alllele frequency from exome-seq bam
allele-frequency
exome
variant
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Chirag Nepal
★ 2.4k
1
vote
0
replies
3.1k
views
Varscan Filtering scripts: very little overlap between output of varscan filtering scripts
snv
exome
varscan
filter-varscan
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Chirag Nepal
★ 2.4k
3
votes
7
replies
3.8k
views
muTect analysis, error
exome
mutect
software-error
updated 2.1 years ago by
Ram
43k • written 9.5 years ago by
Chirag Nepal
★ 2.4k
1
vote
3
replies
5.9k
views
hg19_cosmic_v54_120711.vcf for mutect analysis
mutect
exome
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
Chirag Nepal
★ 2.4k
5
votes
1
reply
4.9k
views
CIGAR M operator maps off end of reference
CIGAR
Exome
updated 3.1 years ago by
Ram
43k • written 9.5 years ago by
Chirag Nepal
★ 2.4k
0
votes
1
reply
1.7k
views
Ribosome protected fragments on CDS V/S UTR
Ribosome-Protected-Fragments
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Chirag Nepal
★ 2.4k
5
votes
5
replies
6.0k
views
Pair-end reads are merged into single file: need to separate
Paired-end-reads
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Chirag Nepal
★ 2.4k
3
votes
3
replies
3.5k
views
Determine inner mate distance and insert size of Pair end reads
exome
paired-end
bowtie
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Chirag Nepal
★ 2.4k
2
votes
3
replies
3.2k
views
Varscan2: run in parallel / merge mpile output from diff run into single mpileup
exome
SNP
varcsan
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Chirag Nepal
★ 2.4k
0
votes
0
replies
2.0k
views
Concat multiple CDS and binning, to show relative position of SNP in CDs. How to?
SNPS
binning
CDS
updated 2.6 years ago by
Ram
43k • written 10.0 years ago by
Chirag Nepal
★ 2.4k
8
votes
5
replies
2.7k
views
Overlaid XY plot with two different colors for control and target genes
RNA-Seq
R
updated 2.6 years ago by
Ram
43k • written 10.0 years ago by
Chirag Nepal
★ 2.4k
4
votes
3
replies
7.6k
views
How To Smooth Ecdf Plot
10.2 years ago by
Chirag Nepal
★ 2.4k
3
votes
3
replies
4.8k
views
How To Extract Alignment With Mismatches From Bowtie Mapping
bowtie
bam
10.5 years ago by
Chirag Nepal
★ 2.4k
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