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Showing :
questions
4
votes
4
replies
6.4k
views
How To Prepare Gatk .Vcf Files Output For Annovar ?
variant
calling
gatk
annovar
vcf
updated 21 months ago by
Ram
43k • written 10.7 years ago by
newDNASeqer
▴ 760
7
votes
4
replies
6.5k
views
In Rna-Seq Data, How To Separate Intronic, Exonic, Non-Coding, Snornas ?
rna
updated 3.2 years ago by
Biostar
20 • written 10.0 years ago by
newDNASeqer
▴ 760
1
vote
5
replies
10k
views
What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
bed
agilent
gatk
updated 4.1 years ago by
Karma
▴ 310 • written 10.3 years ago by
newDNASeqer
▴ 760
0
votes
1
reply
3.7k
views
Tophat Error: It Tries To Execute Lines In Fastq Files
tophat
bowtie
error
updated 4.5 years ago by
Biostar
20 • written 10.7 years ago by
newDNASeqer
▴ 760
0
votes
4
replies
3.8k
views
Tophat Error - What Does This Mean?
tophat
error
bowtie
updated 5.0 years ago by
Biostar
20 • written 10.6 years ago by
newDNASeqer
▴ 760
2
votes
7
replies
8.7k
views
How To Filter Vcf By Coverage?
vcf
coverage
updated 6.7 years ago by
aadeokar
• 0 • written 10.0 years ago by
newDNASeqer
▴ 760
4
votes
11
replies
4.4k
views
How to make this kind of 3-D plotting for cancer subclones ? (picture attached)
subclone
cancer
heterogeneity
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
newDNASeqer
▴ 760
28
votes
13
replies
16k
views
10 follow
Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
gatk
updated 7.5 years ago by
daniel
▴ 30 • written 10.6 years ago by
newDNASeqer
▴ 760
29
votes
19
replies
34k
views
12 follow
Trimming Adapters
adaptor
hiseq
updated 8.4 years ago by
Shicheng Guo
★ 9.4k • written 10.7 years ago by
newDNASeqer
▴ 760
6
votes
2
replies
4.9k
views
annotating MAF files
MAF
annotation
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
newDNASeqer
▴ 760
2
votes
3
replies
4.0k
views
Inferring zygosity information from MAF
MAF
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
newDNASeqer
▴ 760
2
votes
3
replies
3.9k
views
Dissecting number of forward/reverse reads from GATK output
reads
gatk
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
newDNASeqer
▴ 760
5
votes
2
replies
3.5k
views
Downloadable database for human pathways and the associated genes
pathway
database
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
newDNASeqer
▴ 760
4
votes
3
replies
5.1k
views
How To Convert Hg19_Known_Gene From Text Format To Gtf Or Bed?
hg19
bed
format
conversion
gtf
updated 9.8 years ago by
Kamil
★ 2.3k • written 10.6 years ago by
newDNASeqer
▴ 760
3
votes
5
replies
6.6k
views
What is ref sequence name in BAM file header ?
cn.mops
cnv
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
newDNASeqer
▴ 760
3
votes
2
replies
5.3k
views
Tools For Analyzing Copy Number Variation On All-Tumor Exome-Seq Samples
exome
cnv
updated 10.0 years ago by
Ryan D
★ 3.4k • written 10.0 years ago by
newDNASeqer
▴ 760
2
votes
6
replies
3.2k
views
Visualizing Cancer Heterogeneity Results From Ngs Data
cancer
visualization
ngs
updated 10.0 years ago by
Chris Miller
22k • written 10.0 years ago by
newDNASeqer
▴ 760
3
votes
2
replies
8.6k
views
Search A Dna Sequence Motif In Bam File?
motif
dna
bam
updated 10.0 years ago by
JC
13k • written 10.0 years ago by
newDNASeqer
▴ 760
7
votes
4
replies
6.5k
views
Practice Of Filtering Vcf Files (From Gatk)
filter
vcf
gatk
updated 10.1 years ago by
donfreed
★ 1.6k • written 10.1 years ago by
newDNASeqer
▴ 760
2
votes
1
reply
8.8k
views
How To Create A .Bed File With A Few Candidate Genes?
gene
updated 10.2 years ago by
DG
7.3k • written 10.2 years ago by
newDNASeqer
▴ 760
5
votes
5
replies
6.8k
views
How Do You Usually Filter Variant Calling Results?
filter
updated 10.2 years ago by
Alex Paciorkowski
3.5k • written 10.2 years ago by
newDNASeqer
▴ 760
1
vote
2
replies
2.6k
views
Large Data Set Analysis With Cuffdiff
cuffdiff
rnaseq
updated 2.1 years ago by
Ram
43k • written 10.2 years ago by
newDNASeqer
▴ 760
0
votes
1
reply
2.4k
views
How To Calculate What Gene Expression Is Significant In Cuffdiff
cuffdiff
10.4 years ago by
newDNASeqer
▴ 760
0
votes
1
reply
2.4k
views
How To Merge Cuffdiff (Gene_Exp.Diff) Results From Two Batches Or Rnaseq Data?
cuffdiff
cuffmerge
updated 10.5 years ago by
seidel
11k • written 10.5 years ago by
newDNASeqer
▴ 760
1
vote
2
replies
3.6k
views
Cuffdiff Error With Mouse Mm9 Genome Reference
cuffdiff
updated 10.5 years ago by
Devon Ryan
104k • written 10.5 years ago by
newDNASeqer
▴ 760
0
votes
1
reply
2.6k
views
Cuffmerge Error
cuffmerge
updated 10.5 years ago by
Devon Ryan
104k • written 10.5 years ago by
newDNASeqer
▴ 760
3
votes
1
reply
4.2k
views
Qscript Example For Pipelining Gatk With Queue
gatk
updated 10.5 years ago by
Johan
▴ 890 • written 10.5 years ago by
newDNASeqer
▴ 760
1
vote
2
replies
2.1k
views
Tophat: Option --Bowtie Not A Unique Prefix
tophat
bowtie
updated 10.5 years ago by
jeales
▴ 110 • written 10.5 years ago by
newDNASeqer
▴ 760
1
vote
5
replies
4.9k
views
Tophat - Bowtie 1: Index Error? What'S Wrong?
bowtie
updated 2.4 years ago by
Ram
43k • written 10.5 years ago by
newDNASeqer
▴ 760
2
votes
5
replies
4.3k
views
How To Merge Cuffdiff Results To Make A Big Table?
cuffdiff
updated 10.5 years ago by
seidel
11k • written 10.5 years ago by
newDNASeqer
▴ 760
100
votes
9
replies
126k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 23 months ago by
henry-keen
▴ 40 • written 10.5 years ago by
newDNASeqer
▴ 760
3
votes
2
replies
4.2k
views
Help Needed With Annovar - Csv Summary
annovar
vcf
updated 10.6 years ago by
Alex Paciorkowski
3.5k • written 10.6 years ago by
newDNASeqer
▴ 760
5
votes
2
replies
3.1k
views
Why # Of Reads From Accepted_Hits.Bam + Unmapped.Bam > # Of Reads In Fastq File?
tophat
fastq
reads
updated 10.6 years ago by
S_Z
▴ 30 • written 10.6 years ago by
newDNASeqer
▴ 760
19
votes
15
replies
10k
views
12 follow
How To Split Reads For Different Flowcell Lanes In Fastq Files?
split
reads
updated 4 months ago by
steve
★ 3.5k • written 10.7 years ago by
newDNASeqer
▴ 760
16
votes
6
replies
13k
views
Vcf File --> Gene/Protein Mutation Information
vcf
mutation
annovar
updated 10.7 years ago by
Alex Paciorkowski
3.5k • written 10.7 years ago by
newDNASeqer
▴ 760
3
votes
5
replies
4.9k
views
Analyzing Unaligned Sequence (From Bowtie)
bowtie
updated 10.7 years ago by
swbarnes2
14k • written 10.7 years ago by
newDNASeqer
▴ 760
7
votes
3
replies
5.1k
views
Paper Or Detailed Tutorial For Dna Variant Calling Pipeline? Need Help To Start
dna
variant
calling
pipeline
updated 10.7 years ago by
rob234king
▴ 610 • written 10.7 years ago by
newDNASeqer
▴ 760
0
votes
3
replies
2.3k
views
Please Help Interpret Picard Bamindexstats Results
picard
statistics
bwa
updated 10.7 years ago by
always_learning
★ 1.1k • written 10.7 years ago by
newDNASeqer
▴ 760
13
votes
8
replies
11k
views
6 follow
How To Interprete/Display .Vcf Data File?
vcf
variant
calling
updated 10.7 years ago by
alaincoletta
▴ 160 • written 10.7 years ago by
newDNASeqer
▴ 760
1
vote
5
replies
11k
views
Paired-End Reads Alignment For Variant Calling ?
paired-end
variant
calling
gatk
picard
updated 10.7 years ago by
Ashutosh Pandey
12k • written 10.7 years ago by
newDNASeqer
▴ 760
7
votes
5
replies
9.5k
views
Best Human Genome Reference File For Gatk?
gatk
reference
bwa
updated 10.7 years ago by
Matt Shirley
10k • written 10.7 years ago by
newDNASeqer
▴ 760
4
votes
3
replies
5.4k
views
Bwa - Picard - Gatk Pipeline: How To Set The "-M (Mismatch Penalty)" Option For Bwa?
bwa
picard
gatk
updated 10.7 years ago by
matted
7.8k • written 10.7 years ago by
newDNASeqer
▴ 760
2
votes
3
replies
6.9k
views
Where To Download Refseq Mrna Sequence Data?
refseq
updated 10.7 years ago by
Charles Warden
8.2k • written 10.7 years ago by
newDNASeqer
▴ 760
5
votes
1
reply
4.1k
views
Where Can I Download Gatk 2.5 Version?
gatk
updated 12 months ago by
Ram
43k • written 10.7 years ago by
newDNASeqer
▴ 760
44 results • Page
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