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Showing :
questions
1
vote
2
replies
882
views
why GATK and BCFTOOLS output different number of DP
miseq
SNP
4.0 years ago by
bxia
▴ 180
0
votes
0
replies
652
views
How does bcftools estimate the probability for genotype for VAF 0.75 for diploid?
bcftools
snps
genotype
4.0 years ago by
bxia
▴ 180
5
votes
12
replies
7.8k
views
bedGrapthToBigWig conversion, xxx is not found in chromosome files
ChIP-Seq
updated 4.2 years ago by
max
▴ 50 • written 7.9 years ago by
bxia
▴ 180
0
votes
1
reply
3.7k
views
ATCC Cell lines information, Database access
RNA-Seq
updated 5.1 years ago by
Amos Bairoch
▴ 120 • written 7.2 years ago by
bxia
▴ 180
4
votes
4
replies
4.4k
views
Interpretation of TCGA clinical data
RNA-Seq
updated 5.4 years ago by
igor
13k • written 7.8 years ago by
bxia
▴ 180
2
votes
2
replies
4.4k
views
Blast multiple sequences with Biopython qblast
blast
updated 5.8 years ago by
hielkewalinga
▴ 10 • written 7.0 years ago by
bxia
▴ 180
3
votes
5
replies
1.2k
views
How to know favorite and unfavorite for survival analysis programmly?
RNA-Seq
updated 5.9 years ago by
Kristoffer Vitting-Seerup
★ 4.0k • written 5.9 years ago by
bxia
▴ 180
0
votes
1
reply
887
views
edgeR 2GB table
RNA-Seq
5.9 years ago by
bxia
▴ 180
4
votes
4
replies
3.3k
views
how to convert SGD standard name to SGD systematic ID?
SGD
6.1 years ago by
bxia
▴ 180
0
votes
1
reply
1.4k
views
How does WGS normalization perform between samples
whole genome sequencing
6.1 years ago by
bxia
▴ 180
0
votes
6
replies
2.3k
views
LUMPY SV call without quality score
WGS
6.1 years ago by
bxia
▴ 180
6
votes
18
replies
8.7k
views
9 follow
FastQC stuck at 95% read sequences forever
RNA-Seq
updated 6.1 years ago by
fadimeoztoprak
▴ 20 • written 7.9 years ago by
bxia
▴ 180
0
votes
2
replies
1.2k
views
cpath is not available for cytoscape?
protein interaction
updated 6.2 years ago by
cannin
▴ 350 • written 6.2 years ago by
bxia
▴ 180
12
votes
10
replies
4.5k
views
How Gro-seq identify enhancer RNA?
RNA-Seq
updated 6.4 years ago by
Friederike
8.9k • written 6.4 years ago by
bxia
▴ 180
0
votes
1
reply
1.5k
views
Could I map strand specific RNA-seq with non-strand specific?
RNA-Seq
updated 6.6 years ago by
Renesh
★ 2.2k • written 6.6 years ago by
bxia
▴ 180
4
votes
9
replies
11k
views
fastq-dump timeout exhausted error
sra
updated 21 months ago by
Akanksha
• 0 • written 7.0 years ago by
bxia
▴ 180
1
vote
1
reply
1.6k
views
What is the difference between hg19 v9 vs hg19
RNA-Seq
updated 6.6 years ago by
Denise CS
★ 5.2k • written 6.6 years ago by
bxia
▴ 180
1
vote
0
replies
874
views
how do I know there is alternative transcript switch in RNA-seq
RNA-Seq
updated 6.7 years ago by
Biostar
20 • written 6.8 years ago by
bxia
▴ 180
6
votes
7
replies
10.0k
views
how do I know the breast cancer subtype based on TCGA clinical data
RNA-Seq
updated 6.9 years ago by
xushutan
▴ 40 • written 7.8 years ago by
bxia
▴ 180
9
votes
6
replies
3.2k
views
How to know a RNA-seq is polyA or total-RNA-seq in GEO?
GEO
RNA-Seq
updated 6.9 years ago by
Devon Ryan
104k • written 6.9 years ago by
bxia
▴ 180
2
votes
5
replies
2.7k
views
bed format, START always bigger than END, no matter which strand?
bed
bowtie
updated 6.9 years ago by
Alex Reynolds
35k • written 6.9 years ago by
bxia
▴ 180
1
vote
3
replies
1.0k
views
Encode http 403 error, I am being blocked?
RNA-Seq
7.0 years ago by
bxia
▴ 180
0
votes
1
reply
1.4k
views
paired sample in ENCODE RNA-seq and ChIP-seq
encode
7.0 years ago by
bxia
▴ 180
0
votes
1
reply
1.4k
views
Is there a function similar with qblast to blast the SeqIO.parse object? Biopython Blastn
blast
7.0 years ago by
bxia
▴ 180
0
votes
3
replies
1.3k
views
HTseq report 80% of reads no feature
RNA-Seq
updated 7.0 years ago by
Devon Ryan
104k • written 7.0 years ago by
bxia
▴ 180
3
votes
4
replies
1.3k
views
Is there a way that I can perform blast through NCBI from my program?
blast
updated 7.1 years ago by
Pierre Lindenbaum
161k • written 7.1 years ago by
bxia
▴ 180
0
votes
1
reply
1.7k
views
submission template for Bioinformatics
article
7.1 years ago by
bxia
▴ 180
1
vote
1
reply
2.1k
views
Does MACS2 or MACS14 perform total reads normalization?
ChIP-Seq
updated 7.1 years ago by
Biostar
20 • written 7.1 years ago by
bxia
▴ 180
0
votes
2
replies
1.2k
views
bowtie no reported alignment?
ChIP-Seq
7.1 years ago by
bxia
▴ 180
0
votes
2
replies
1.1k
views
Do I need to only keep exon in gene GTF when I run Cuffdiff?
RNA-Seq
updated 7.2 years ago by
Petr Ponomarenko
★ 2.8k • written 7.2 years ago by
bxia
▴ 180
9
votes
17
replies
7.0k
views
8 follow
The most popular Alternative to David?
RNA-Seq
updated 7.2 years ago by
Girolamo
▴ 140 • written 7.2 years ago by
bxia
▴ 180
1
vote
5
replies
1.8k
views
Tophat2 very high percentage of multiple alignments
RNA-Seq
7.3 years ago by
bxia
▴ 180
0
votes
2
replies
4.1k
views
fastq dump error: ERROR:106: Magic cookie '#%Module' missing
RNA-Seq
7.4 years ago by
bxia
▴ 180
7
votes
4
replies
4.8k
views
Why chip-seq is strand specific?
ChIP-Seq
updated 7.4 years ago by
spacemorrissey
▴ 280 • written 7.4 years ago by
bxia
▴ 180
2
votes
7
replies
17k
views
how to get values from a columns from atomic vector without get the names of rows?
R
updated 7.4 years ago by
ddiez
★ 2.0k • written 7.5 years ago by
bxia
▴ 180
2
votes
8
replies
3.1k
views
different BED Format for peak calling
ChIP-Seq
written 7.6 years ago by
bxia
▴ 180
0
votes
2
replies
1.5k
views
Clinical Data Analysis, Should compared with Normal tissue?
RNA-Seq
7.8 years ago by
bxia
▴ 180
7
votes
7
replies
2.0k
views
Main difference between format of Ensembl and USCS annotation
RNA-Seq
Ensembl
UCSC
updated 7.8 years ago by
Emily
23k • written 7.8 years ago by
bxia
▴ 180
3
votes
2
replies
4.5k
views
what is the '.' , '+' means in GTF file
RNA-Seq
updated 7.8 years ago by
SES
8.6k • written 7.8 years ago by
bxia
▴ 180
6
votes
1
reply
2.7k
views
HTSEQ count is the raw count, not RPKM or FPKM, right?
RNA-Seq
updated 7.8 years ago by
WouterDeCoster
47k • written 7.8 years ago by
bxia
▴ 180
3
votes
6
replies
3.3k
views
GENECODE V24 vs V22 vs V19
RNA-Seq
gencode
updated 7.8 years ago by
EagleEye
7.5k • written 7.8 years ago by
bxia
▴ 180
7
votes
7
replies
3.5k
views
which annotation I should for RNA-seq? Ensembl, UCSC or refseq?
RNA-Seq
Ensembl
RefSeq
updated 7.9 years ago by
Denise CS
★ 5.2k • written 7.9 years ago by
bxia
▴ 180
1
vote
7
replies
1.6k
views
high aligned_not_unique number for HTSeq
RNA-Seq
7.9 years ago by
bxia
▴ 180
1
vote
8
replies
2.9k
views
HTSeq result, most genes have 0 count?
RNA-Seq
7.9 years ago by
bxia
▴ 180
3
votes
2
replies
2.0k
views
Do I need to remove unmapped reads before running MACS2?
ChIP-Seq
updated 7.9 years ago by
Ming Tommy Tang
★ 3.9k • written 7.9 years ago by
bxia
▴ 180
8
votes
2
replies
2.3k
views
Why samtools sort input file is 4.3 Gb but output become 3.5Gb....
ChIP-Seq
updated 7.9 years ago by
John
13k • written 7.9 years ago by
bxia
▴ 180
1
vote
4
replies
1.5k
views
where I can download mapped result of SRA files
ChIP-Seq
updated 7.9 years ago by
Shicheng Guo
★ 9.4k • written 7.9 years ago by
bxia
▴ 180
2
votes
3
replies
2.3k
views
For Chip-seq, which control data I should choose for each biological replicate samples in MACS2
Chip-seq
updated 7.9 years ago by
James Ashmore
★ 3.4k • written 7.9 years ago by
bxia
▴ 180
2
votes
6
replies
1.8k
views
Does bowtie2 still require fastqsanger format?
ChIP-Seq
updated 7.9 years ago by
Steven Lakin
★ 1.8k • written 7.9 years ago by
bxia
▴ 180
2
votes
6
replies
2.0k
views
Primary_assembly and GRCh38.84.gtf.gz are the files for mapping?
RNA-Seq
ChIP-Seq
updated 7.9 years ago by
Denise CS
★ 5.2k • written 7.9 years ago by
bxia
▴ 180
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