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Showing :
questions
3
votes
3
replies
7.5k
views
How to plot length distribution of contigs in the assembly?
plotting
assembly
length-distribution
updated 2.6 years ago by
Ram
45k • written 9.6 years ago by
seta
★ 1.9k
1
vote
2
replies
4.0k
views
Combining snp and indel vcf files with GATK4
varint calling
GATK4
combin variant
SortVcf
updated 6.6 years ago by
harold.smith.tarheel
★ 5.0k • written 6.6 years ago by
seta
★ 1.9k
0
votes
6
replies
1.7k
views
Extracting genomic coordinate, feature type and strand for a gene list
gene list
genomic coordinate
feature type
6.6 years ago by
seta
★ 1.9k
0
votes
2
replies
2.0k
views
Access to HMMER software
alignment
protein
domain
HMMAER
updated 2.8 years ago by
Ram
45k • written 9.2 years ago by
seta
★ 1.9k
7
votes
6
replies
3.1k
views
Why there are some discrepancies between VEP output and "variation" section of Ensembl?!
SNP
VEP output
alternative allele
Ensembl
updated 6.6 years ago by
zx8754
12k • written 6.8 years ago by
seta
★ 1.9k
2
votes
7
replies
3.0k
views
blast running for several splitted query
blast
alignment
RNA-Seq
updated 2.2 years ago by
Ram
45k • written 10.0 years ago by
seta
★ 1.9k
6
votes
19
replies
5.5k
views
Getting allele frequency and zygosity information from several vcf file
vcf
allele frequency
zygocity
updated 6.6 years ago by
Kevin Blighe
89k • written 6.6 years ago by
seta
★ 1.9k
4
votes
9
replies
5.0k
views
Hard filtering results of vcf file for multiple samps
variant calling
GATK
hard filtering
updated 6.7 years ago by
finswimmer
16k • written 6.7 years ago by
seta
★ 1.9k
1
vote
2
replies
2.6k
views
Applying BQSR before running GATK's HaplotypeCaller on whole-genome sequencing data
variant calling
HaplotypeCaller
updated 6.7 years ago by
finswimmer
16k • written 6.7 years ago by
seta
★ 1.9k
13
votes
9
replies
18k
views
how to extract best hits of blast in terms of e-value, identity,...?
blast
RNA-Seq
alignment
updated 2.3 years ago by
Ram
45k • written 9.9 years ago by
seta
★ 1.9k
14
votes
20
replies
3.5k
views
Please suggest an appropriate genome-guided transcriptome assembler
RNA-Seq
genome
alignment
marker
updated 6.8 years ago by
Kevin Blighe
89k • written 6.9 years ago by
seta
★ 1.9k
0
votes
1
reply
2.4k
views
Error with alignReads.pl in Trinity?
Assembly
RNA-Seq
next-gen-sequencing
updated 2.5 years ago by
Ram
45k • written 9.8 years ago by
seta
★ 1.9k
0
votes
4
replies
1.3k
views
Please provide me your comments on the variant calling in this case
variant calling
genome sequencing
6.9 years ago by
seta
★ 1.9k
0
votes
4
replies
3.5k
views
Poly A trimming from RNA-seq data by bbduk (bbmap package)
polyA
trimming
RNA-seq
bbduk
bbmap
updated 6.9 years ago by
WouterDeCoster
47k • written 6.9 years ago by
seta
★ 1.9k
3
votes
2
replies
1.9k
views
Is haplotype phasing essential after variant calling?
haplotype phasing
genome sequencing
updated 7.0 years ago by
WouterDeCoster
47k • written 7.0 years ago by
seta
★ 1.9k
3
votes
4
replies
1.7k
views
Aligning short reads to a human specific gene instead of reference genome
alignment
human reference genome
7.0 years ago by
seta
★ 1.9k
2
votes
4
replies
1.5k
views
Please suggest your idea for variant calling analysis of many BAM files from whole genome sequencing
variant calling
alingnment
whole genome sequencing
updated 7.0 years ago by
finswimmer
16k • written 7.0 years ago by
seta
★ 1.9k
2
votes
2
replies
3.6k
views
k-mer optimization in Trinity
RNA-Seq
Assembly
next-gen
updated 7.0 years ago by
snek
• 0 • written 10.4 years ago by
seta
★ 1.9k
1
vote
10
replies
8.9k
views
How to change fastq reads header for running Trinity on them?
trinity
RNA-Seq
ngs
Assembly
updated 2.2 years ago by
Ram
45k • written 10.0 years ago by
seta
★ 1.9k
2
votes
7
replies
5.6k
views
Please adivse me on differential expression analysis on the STAR/Stringtie output
differential expression
STAR
stringtie
count
edgeR
updated 7.1 years ago by
Biostar
20 • written 8.2 years ago by
seta
★ 1.9k
0
votes
5
replies
4.6k
views
threshold of bonferroni-corrected p-value
RNA-Seq
R
updated 3.1 years ago by
Ram
45k • written 10.4 years ago by
seta
★ 1.9k
0
votes
0
replies
2.4k
views
Cuffcompare on the merged GTF file produced by Stringtie
Cufflinks
Stringtie
splicing
cuffdiff
updated 7.3 years ago by
Biostar
20 • written 8.1 years ago by
seta
★ 1.9k
4
votes
5
replies
3.9k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 12 months ago by
Ram
45k • written 7.3 years ago by
seta
★ 1.9k
2
votes
2
replies
1.2k
views
Please help to understand the concept of the sentence about cufflinks
cufflinks
likelihood function
RNA-Seq
updated 7.3 years ago by
Kevin Blighe
89k • written 7.3 years ago by
seta
★ 1.9k
1
vote
2
replies
1.8k
views
miRNA-seq pipeline in biostar handbook?
miRNA-seq
Biostar handbook
updated 7.3 years ago by
Istvan Albert
102k • written 7.3 years ago by
seta
★ 1.9k
6
votes
9
replies
12k
views
Issue with installing bowtie2
bowtie2
installing
error
updated 7.5 years ago by
Karma
▴ 310 • written 8.2 years ago by
seta
★ 1.9k
0
votes
10
replies
4.8k
views
Issue with bowtie2-align during installation of bowtie2
bowtie2
bowtie2-align
installation
updated 7.5 years ago by
Karma
▴ 310 • written 8.2 years ago by
seta
★ 1.9k
0
votes
5
replies
2.7k
views
Regarding TMM normalization before DEG analysis by DEGseq
TMM
DEGseq
DEG analysis
updated 7.6 years ago by
theobroma22
★ 1.2k • written 7.6 years ago by
seta
★ 1.9k
2
votes
5
replies
8.6k
views
Getting FPKM value from edgeR software
edgeR
FPKM value
error
updated 7.8 years ago by
Biostar
20 • written 8.5 years ago by
seta
★ 1.9k
0
votes
2
replies
1.4k
views
The same results with various dataset by cufflinks
mapping
alignment
assembly
cufflinks
7.9 years ago by
seta
★ 1.9k
1
vote
4
replies
1.6k
views
inner and outer genomic coordinates concept
genome alignment
coordinate
outer
updated 7.9 years ago by
h.mon
35k • written 7.9 years ago by
seta
★ 1.9k
1
vote
1
reply
1.6k
views
Please help me with the fate of multimapping reads in the RNA-seq context
RNA-Seq
multimapping
7.9 years ago by
seta
★ 1.9k
3
votes
6
replies
5.9k
views
Please help me with pyfasta
fasta
pyfasta
updated 2.1 years ago by
Ram
45k • written 9.1 years ago by
seta
★ 1.9k
0
votes
1
reply
2.4k
views
Issue with gffread during converting gtf file to fasta
fasta
gtf
gffread
updated 2.1 years ago by
Ram
45k • written 7.9 years ago by
seta
★ 1.9k
0
votes
3
replies
3.7k
views
FastX Collapser and duplicate removal
ngs
read
duplicate
Fastx collapser
7.9 years ago by
seta
★ 1.9k
0
votes
1
reply
2.3k
views
Sliding window in Trimmomatic and PrinSeq
trimming
sliding window
8.0 years ago by
seta
★ 1.9k
1
vote
2
replies
3.3k
views
Command to estimate how long local blastx take to finish the job?
blast
RNA-Seq
alignment
updated 2.8 years ago by
Ram
45k • written 10.0 years ago by
seta
★ 1.9k
0
votes
2
replies
1.9k
views
Please advise me on PE sequencing reads prepared by NEBNex kit and Hiseq2000
NEBNex kit
Illumina
Fastqc
adapter
length
8.0 years ago by
seta
★ 1.9k
1
vote
9
replies
5.1k
views
Modification of fastq header
header
fastq
read
modification
updated 8.0 years ago by
Charles Plessy
★ 2.9k • written 8.0 years ago by
seta
★ 1.9k
0
votes
0
replies
1.4k
views
QIEA and CRO algorithms for assembly of sequencing reads produced by NGS technology
algorithm
assembly
reads
NGS
8.1 years ago by
seta
★ 1.9k
0
votes
0
replies
1.8k
views
adding tss_id and p_id to GTF file by cuffdiff_gtf_attributes
cuffdiff
RNA-seq
GTF
updated 2.1 years ago by
Ram
45k • written 8.1 years ago by
seta
★ 1.9k
6
votes
7
replies
3.5k
views
Extracting fasta sequences with identical header
fasta
extracting
identical header
updated 8.1 years ago by
Brian Bushnell
20k • written 8.1 years ago by
seta
★ 1.9k
0
votes
7
replies
2.2k
views
SSR marker discovery from RNA-seq data when a reference genome is available
SSR
RNA-se
genome
alignment
8.1 years ago by
seta
★ 1.9k
0
votes
2
replies
1.8k
views
SSR marker discovery from BAM/SAM input file
BAM
genome alignment
simple sequence repeat
8.2 years ago by
seta
★ 1.9k
1
vote
4
replies
3.1k
views
How do you find ballgown package for differential expression analysis?
differential expression
ballgown
8.2 years ago by
seta
★ 1.9k
0
votes
8
replies
2.7k
views
An odd error with StringTie!!
stringtie
rnaseq
error
updated 8.2 years ago by
Devon Ryan
105k • written 8.2 years ago by
seta
★ 1.9k
3
votes
6
replies
4.6k
views
The right pipline with cufflinks, cuffmerge and cuffdiff
cufflinks
annotation
cuffdiff
updated 8.2 years ago by
WouterDeCoster
47k • written 8.2 years ago by
seta
★ 1.9k
0
votes
11
replies
3.7k
views
how to get corresponding transcript/gene sequence from aligned reads to human genome?
alignment
bam
referene genome
human
8.2 years ago by
seta
★ 1.9k
3
votes
3
replies
1.6k
views
Where I find plant example (small) dataset from Illumina Hiseq 2000 sequencing
Illumina
example dataset
updated 8.3 years ago by
Abdul Rafay Khan
★ 1.2k • written 8.3 years ago by
seta
★ 1.9k
2
votes
6
replies
2.9k
views
Trouble with installation Trinity on Linux 32 bit
Trinity
software installation
updated 8.3 years ago by
Farbod
★ 3.4k • written 8.3 years ago by
seta
★ 1.9k
294 results • Page
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