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19 results • Page
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8
votes
8
replies
591
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 hour ago by
Philipp Bayer
8.3k • written 19 hours ago by
noodle
▴ 530
1
vote
7
replies
362
views
gvcf joint calling
WES
GATK
VCF
gVCF
5 hours ago by
zihanss
• 0
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 6 hours ago by
Ram
43k • written 8 months ago by
Calum
▴ 10
0
votes
6
replies
157
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
40 minutes ago by
Ruqaiya
• 0
0
votes
5
replies
320
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 23 hours ago by
Istvan Albert
100k • written 4 days ago by
sehriban.buyukkilic
▴ 10
2
votes
3
replies
2.5k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 12 hours ago by
zihanss
• 0 • written 23 months ago by
Vitor1
▴ 120
1
vote
3
replies
270
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 13 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
2
votes
3
replies
256
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 20 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
1
vote
2
replies
127
views
How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
1 hour ago by
Francesco
▴ 10
0
votes
2
replies
272
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 19 hours ago by
Jesse
▴ 740 • written 3 days ago by
Broccoli
• 0
1
vote
2
replies
273
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
17 hours ago by
Francesco
▴ 10
0
votes
1
reply
261
views
absolute path for symbolic links in Snakefile
Snakemake
updated 19 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
1
vote
1
reply
152
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 6 hours ago by
ATpoint
82k • written 1 day ago by
vanbelj
▴ 40
0
votes
1
reply
657
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 2 hours ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
0
votes
0
replies
74
views
Filter low express genes in microarray data
microarray
18 hours ago by
Chris
▴ 260
0
votes
0
replies
72
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
17 hours ago by
tnminh89
▴ 10
0
votes
0
replies
42
views
adjusting for confounders in LMER in R
confounders
LMER
R
7 hours ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
78
views
Extract protein sequence
fasta
alighment
blast
18 hours ago by
anna
▴ 20
0
votes
0
replies
29
views
Downloading full alignments from Pfam
pfam
2 hours ago by
bef1
• 0
19 results • Page
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Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
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
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Recent Replies
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.3k
While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
1. What does clipped Fastq mean? both forward and reverse reads in the same file? 2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right? I'l try spades. [1]: http…
Comment: How to assign cell types after integration in scRNA
by
Francesco
▴ 10
Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
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
▴ 530
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
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