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73 results • Page
1 of 2
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Views
Votes
Replies
0
votes
0
replies
25
views
BEDOPS convert2bed output
vcf
bedops
convert2bed
bed
3 hours ago by
nehaklkn
• 0
0
votes
1
reply
36
views
How to calculate position-specific fastq stats?
rnaseq
fastq
metagenomics
genomics
updated just now by
GenoMax
118k • written 5 hours ago by
O.rka
▴ 610
0
votes
0
replies
31
views
Finding Specific Types of Data for Cancer Studies
TCGA
GDC
Cancer
Entrez
GEO
6 hours ago by
Vincent Laufer
★ 2.2k
0
votes
0
replies
61
views
Should the repressor really have a negative correlation with its motif?
atac-seq
scatac-seq
single-cell
5 hours ago by
Janus
• 0
1
vote
0
replies
56
views
How does LUMPY report breakpoints in multiple samples?
lumpy
SV
breakpoint
variation
structural
SVs
10 hours ago by
Getting there
▴ 80
2
votes
2
replies
106
views
Reference counts for RNA-seq
expression
rna
rna-seq
tpm
transcripts
updated 2 hours ago by
Giovanni M Dall'Olio
27k • written 18 hours ago by
syntax
▴ 70
0
votes
1
reply
68
views
Time Treatment analysis on Rna-Seq
R
GEO
Rna-seq
updated 19 hours ago by
Matthias Zepper
★ 1.4k • written 20 hours ago by
ShowPow
▴ 20
1
vote
0
replies
49
views
KissDE and batch effect
kissDE
kissplice
20 hours ago by
david.b.rombaut
▴ 10
0
votes
0
replies
52
views
Zenodo command line uploads
zenodo
updated 20 hours ago by
GenoMax
118k • written 21 hours ago by
zhousun21
▴ 40
0
votes
0
replies
56
views
Cytoscape visualisation issue
cytoscape
23 hours ago by
sarah.laverty20
• 0
0
votes
3
replies
120
views
CD4+ and CD8+ T cell classification
Immunology
T
cell
updated 21 hours ago by
antonioggsousa
★ 2.5k • written 1 day ago by
pgangaitkar
• 0
0
votes
1
reply
83
views
Converting RSIDs in the HLA region (e.g.) HLA-A*:01:01g-B*08:01 format?
SNP
HLA
rsid
updated 21 hours ago by
GenoMax
118k • written 1 day ago by
4galaxy77
★ 2.2k
0
votes
5
replies
216
views
GATK's selectVariants not outputting VCF
GATK
updated 20 hours ago by
Pierre Lindenbaum
147k • written 1 day ago by
dec986
▴ 340
0
votes
2
replies
130
views
phylogeny
phylogeny
genes
with
virulence
19 hours ago by
saifulislam99121
• 0
0
votes
0
replies
104
views
calculate meandepths for CDSs after mapping transcriptome reads to the genome
gtf
sam
meandepth
samtools
alignment
6 hours ago by
poecile.pal
▴ 40
1
vote
4
replies
199
views
Bowtie2 doesn't align paired-end sequences
bowtie2
mapping
alignment
updated 20 hours ago by
Ram
36k • written 9 days ago by
Arda
• 0
4
votes
6
replies
287
views
About normalization of the datasets from Harmonized TCGA data
profiling
data
normalisation
transcript
protein
6 hours ago by
qiz218591
▴ 10
1
vote
2
replies
170
views
vg construct unsupported variant allele
vg
graph
vcf
variantion
vgteam
19 hours ago by
Yihang
• 0
0
votes
0
replies
1.7k
views
Sequence read (id) specific kmer frequency calculation
kmer
reads
sequence
metagenome
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
arif.at.iut
• 0
0
votes
1
reply
2.1k
views
How to use Deconseq?
next-gen-sequencing
updated 18 hours ago by
Ram
36k • written 6.7 years ago by
Al
• 0
0
votes
0
replies
1.9k
views
Use Aroma Project to preprocess files for PennCNV
CNA
CNV
aroma
penncnv
updated 14 hours ago by
Ram
36k • written 6.7 years ago by
gaiusjaugustus
▴ 210
1
vote
7
replies
5.3k
views
Blastp -outfmt Problem With Format Specifiers
outfmt
blastp
blast
updated 15 hours ago by
Ram
36k • written 6.7 years ago by
bearbob
• 0
0
votes
3
replies
1.6k
views
abyss PopBubbles error
genome-assembly
abyss
bubbles
updated 16 hours ago by
Ram
36k • written 6.7 years ago by
Damian Kao
16k
0
votes
0
replies
1.0k
views
tophat2 incomplete mapping of reads
RNA-Seq
updated 18 hours ago by
Ram
36k • written 6.7 years ago by
dina.hesham139
▴ 150
0
votes
0
replies
2.5k
views
Problem with big RMSD value, docking
software-error
updated 16 hours ago by
Ram
36k • written 6.7 years ago by
chemistry1233
▴ 50
5
votes
5
replies
1.4k
views
How to determine whether a contig is sex-linked
sequence
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
ecophylic
▴ 20
1
vote
1
reply
1.5k
views
Compiling UniProt txt file into a table of ( AC - ACcession number) and (MOD_RES)
python
uniprot
updated 16 hours ago by
Ram
36k • written 6.7 years ago by
ahmedakhokhar
▴ 150
1
vote
2
replies
1.5k
views
Software for structure prediction for large number of (single) mutations
single-mutation
software
structure
updated 14 hours ago by
Ram
36k • written 6.7 years ago by
rod.god
• 0
6
votes
7
replies
5.5k
views
best alignment tool for Ion Torrent data
chloroplast
genome
iontorrent
updated 15 hours ago by
Ram
36k • written 6.7 years ago by
Ann
★ 2.3k
0
votes
1
reply
1.4k
views
ADNIData training part 2
ARM
DXSUM
ADNI
R
symbol
updated 14 hours ago by
Ram
36k • written 6.7 years ago by
marwa.cs91
▴ 30
0
votes
0
replies
1.9k
views
gDNA annotation, exon and intron boundary identification
gene
sequencing
sequence
updated 18 hours ago by
Ram
36k • written 6.7 years ago by
chethusomashekar
• 0
5
votes
1
reply
4.9k
views
Generating Gencode TSS file
gencode
tss
updated 15 hours ago by
Ram
36k • written 6.7 years ago by
dally
▴ 210
0
votes
0
replies
1.4k
views
short kmer or long kmer with SNP inside ?
parameters
discosnp
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
sebastien.letort
▴ 70
0
votes
2
replies
2.3k
views
maSigPro warnings in glm.fit
rnaseq
glm.fit
masigpro
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
Assa Yeroslaviz
★ 1.7k
5
votes
0
replies
3.5k
views
Interpreting dispersion plots in RNAseq analysis
RNA-Seq
dispersion
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
Shellfishgene
▴ 60
1
vote
2
replies
2.9k
views
Find an existing nucleotide sequence for a specific protein sequence through NCBI eutils
efetch
esearch
eutils
elink
sequence
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
Jenez
▴ 540
2
votes
10
replies
2.9k
views
concatenate multiple GZip fastq files from multilane run and output combined gzip file
perl
fastqc
next-gen-sequencing
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
PAn
▴ 20
0
votes
3
replies
1.7k
views
Psi-BLAST error : During COG analysis
BLAST
COG
Psi-Blast
updated 15 hours ago by
Ram
36k • written 6.7 years ago by
Mohit
▴ 20
0
votes
0
replies
1.9k
views
Fastq file format rejected from RAST server
software-error
next-gen-sequencing
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
vieira.cogu
• 0
0
votes
0
replies
1.4k
views
Determining variant strand from dbSNP entrez document summary
strand
ncbi
eutils
dbsnp
entrez
updated 18 hours ago by
Ram
36k • written 6.7 years ago by
sbrown8
▴ 20
0
votes
0
replies
3.0k
views
Troubleshooting differential expression with limma
limma
microarray
differential-gene-expression
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
deconti.d
• 0
0
votes
0
replies
1.6k
views
Writing a script to analyze similarity between 5 mitochondrial DNA sequences
perl
mtdna
sequence
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
jahanarahoque
• 0
0
votes
0
replies
1.0k
views
Which ligands bind (are sensed by) these Odorant Binding Proteins?
odorant
ligand
protein
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
a1ultima
▴ 820
1
vote
2
replies
1.8k
views
LEON producing truncated output
leon
gatb
fastq
updated 20 hours ago by
Ram
36k • written 6.7 years ago by
intipedroso
▴ 10
0
votes
1
reply
3.2k
views
Conversion effinciency issue in whole genome bisulfite sequencing data.
wgbs
bismark
conversion-efficiency
updated 18 hours ago by
Ram
36k • written 6.7 years ago by
Tori
▴ 90
0
votes
0
replies
1.4k
views
Calculate Khi 2 - GCskew - C programming
GCskew
C
Khi2
updated 19 hours ago by
Ram
36k • written 6.7 years ago by
nathaydania
• 0
3
votes
7
replies
1.3k
views
Why blast doesn't cache previous queries?
blast
updated 18 hours ago by
Ram
36k • written 6.7 years ago by
roy.granit
▴ 880
0
votes
0
replies
1.2k
views
microarray sorting strategy for 40 candidates
sorting
microarray
updated 16 hours ago by
Ram
36k • written 6.7 years ago by
MrT11
• 0
0
votes
1
reply
1.3k
views
How to validate a model obtained from Modeller
3D-structure
modeller
protein
updated 16 hours ago by
Ram
36k • written 6.7 years ago by
thaonguyen8310
• 0
1
vote
5
replies
4.2k
views
MafftCommandline error, doesn't recognize mafft as an internal or external command
mafft
error
alignment
updated 17 hours ago by
Ram
36k • written 6.7 years ago by
erikras1223
▴ 10
73 results • Page
1 of 2
Recent Votes
Answer: How to split paired end SRA file into 2 correct fastq files
Answer: A method to find if a variant is Genomic or an RNA-Editing variant
Answer: Modelling vs removing effects from confounding variables and their uses for down
A: stringtie Error: input file cannot be found
Comment: AF = 0.5 in chrX, VCF of a male
Comment: AF = 0.5 in chrX, VCF of a male
Answer: extracting sequences from a bam file
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Comment: AF = 0.5 in chrX, VCF of a male
by
paolo
▴ 10
My calls for chrX are all in the region between PAR1 and PAR2, so they are not in the pseudoautosomal region.
Answer: A method to find if a variant is Genomic or an RNA-Editing variant
by
i.sudbery
15k
No, not really. Not without access to matched DNA-sequencing form the same individual. [SPRINT][1] claims to be able to identify RNA ed…
Answer: Modelling vs removing effects from confounding variables and their uses for down
by
i.sudbery
15k
Confounders should be modeled where that is possible, not removed. This particularly applies to DE analysis, or anything that relies on cou…
Comment: WGCNA - problem with hclustplot (Human Chimp paper tutorial)
by
annamariabugaj
• 0
Thank you for the clarifying - yes, you are right, I can see the opposite expression levels in the top and bottom of Turquoise heatmap and …
Comment: Genome-wide enrichment of histone marks and correlation with gene expression: Ap
by
Ankit
▴ 350
Hi LChart, Thanks for the suggestions. IntePareto seems good option to start with. The others are machine learning based models which I am…
Comment: Distinguishing records for reads in a pair in a SAM file
by
appropiate
▴ 20
Thanks @d-cameron, yes, multiple alignments for R1 and R2 of the same template have the same name, and I only know how to distinguish if t…
Comment: Distinguishing records for reads in a pair in a SAM file
by
appropiate
▴ 20
Thanks a lot @dariober, you did understand correctly (I could have explained myself better...), just wanted to distinguish between first- a…
Comment: Reference counts for RNA-seq
by
Giovanni M Dall'Olio
27k
That's right, you cannot do DE without samples from the same experiment. At most, you can compare the top expressed genes against the [GTE…
Answer: How to match tumor fastq file to normal fastq file? (I just have a set of tumor
by
tomas4482
▴ 280
Check SRA selector runner for metadata, GEOdataset for metadata, original article for sampling tables or ask the authors. This is not a tec…
Comment: Are upset plots bad for differential expression analysis?
by
paulimer
▴ 10
That's really interesting! Majority vote is indeed a solution, provided I find an elegant way to settle ties. The app will always be used …
Comment: AF = 0.5 in chrX, VCF of a male
by
Pierre Lindenbaum
147k
a BAM is not perfect. If there is any region with a lot of mismatches (bad reads, duplicated regions, low complexity region...) , GATK will…
Answer: Distinguishing records for reads in a pair in a SAM file
by
dariober
13k
If I understand the question correctly, you want to know which of the multiple alignments are from the first-in-pair and which are from the…
Answer: Distinguishing records for reads in a pair in a SAM file
by
d-cameron
★ 2.6k
The [SAM file format specifications][1] states: Multiple mapping The correct placement of a read may be ambiguous, e.g., due to re…
Comment: AF = 0.5 in chrX, VCF of a male
by
d-cameron
★ 2.6k
Are these variants in the pseudoautosomal region?
Answer: Circos plot from SV data of WES samples
by
d-cameron
★ 2.6k
> I'm absolutely new in these waters so I'd very much appreciate some help. There are a number of issues that have the potentially to fund…
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