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20 results • Page
1 of 1
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7
votes
7
replies
554
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
7 hours ago by
noodle
▴ 520
1
vote
7
replies
338
views
gvcf joint calling
WES
GATK
VCF
gVCF
3 hours ago by
zihanss
• 0
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 3 hours ago by
Ram
43k • written 8 months ago by
Calum
▴ 10
0
votes
5
replies
314
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 21 hours ago by
Istvan Albert
100k • written 4 days ago by
sehriban.buyukkilic
▴ 10
4
votes
4
replies
380
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 21 hours ago by
BioinfGuru
★ 1.7k • written 3 days ago by
Ming Tommy Tang
★ 3.9k
2
votes
3
replies
2.5k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 9 hours ago by
zihanss
• 0 • written 23 months ago by
Vitor1
▴ 120
2
votes
3
replies
248
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 17 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
1
vote
3
replies
253
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 10 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
0
votes
2
replies
114
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
updated 6 hours ago by
Ram
43k • written 9 hours ago by
Ruqaiya
• 0
0
votes
2
replies
265
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 17 hours ago by
Jesse
▴ 740 • written 3 days ago by
Broccoli
• 0
1
vote
2
replies
262
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
14 hours ago by
Francesco
▴ 10
0
votes
1
reply
102
views
How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
updated 4 hours ago by
ATpoint
82k • written 14 hours ago by
Francesco
▴ 10
1
vote
1
reply
144
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 hours ago by
ATpoint
82k • written 1 day ago by
vanbelj
▴ 40
0
votes
1
reply
258
views
absolute path for symbolic links in Snakefile
Snakemake
updated 17 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
0
votes
1
reply
636
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 19 minutes ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
0
votes
0
replies
7
views
Downloading full alignments from Pfam
pfam
20 minutes ago by
bef1
• 0
0
votes
0
replies
69
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
14 hours ago by
tnminh89
▴ 10
0
votes
0
replies
69
views
Filter low express genes in microarray data
microarray
16 hours ago by
Chris
▴ 260
0
votes
0
replies
37
views
adjusting for confounders in LMER in R
confounders
LMER
R
4 hours ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
72
views
Extract protein sequence
fasta
alighment
blast
15 hours ago by
anna
▴ 20
20 results • Page
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Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
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Recent Replies
Answer: Can I run cellassign on samples independently if there is batch effect present?
by
Francesco
▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling
by
zihanss
• 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted?
by
ATpoint
82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA
by
ATpoint
82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
• 0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
• 0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
Answer: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing?
by
GenoMax
141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
zihanss
• 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
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