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133 results • Page 1 of 3
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7
votes
16
replies
2.0k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 4 days ago by 38k • written 5.5 years ago by ★ 3.6k
2
votes
8
replies
9.1k
views
Size of typical genomic data
genomic
updated 4 days ago by 38k • written 4.9 years ago by 10k
7
votes
7
replies
528
views
Nextflow rnaseq finishing early
RNA-seq nextflow
updated 3 days ago by 38k • written 3 days ago by ★ 1.4k
6
votes
7
replies
1.1k
views
The size of the genome in pb of an organism before sequencing?
sequencing genome
updated 4 days ago by 38k • written 4.4 years ago by • 0
6
votes
7
replies
4.4k
views
Creation Of A .Bed File From .Txt
plink
updated 4 days ago by 38k • written 9.2 years ago by • 0
0
votes
6
replies
412
views
Kallisto bustools for scRNA-seq
Kallisto
updated 2 days ago by ★ 4.0k • written 4 days ago by ▴ 20
0
votes
5
replies
273
views
featureCounts problem in reading Gff
featureCounts GFF RNA-seq
updated 3 days ago by 38k • written 3 days ago by • 0
0
votes
5
replies
553
views
Python table data extraction
python
updated 4 days ago by 38k • written 7 months ago by • 0
0
votes
4
replies
349
views
RNA Sequencing and Vg pan -transcriptome build
fasta pan-transcriptome pan-genome vg
3 days ago by kcarery • 0
1
vote
4
replies
218
views
Suggestion for approaching multiple conditions scRNA-seq
scRNA-seq
2 days ago by Eisuan ▴ 20
1
vote
4
replies
265
views
Protein name in GenBank
genbank python biopython
updated 5 days ago by 127k • written 5 days ago by • 0
3
votes
4
replies
4.8k
views
How to visualize sequence quality control distribution
sequence Fastq R
updated 15 hours ago by 38k • written 7.4 years ago by ▴ 30
1
vote
4
replies
311
views
Snakemake doesn't recognize output files even though they are created
python Snakemake
12 hours ago by DdogBoss • 0
0
votes
4
replies
416
views
Problem with fatsq-dump
fastq-dump sratoolkit
5 days ago by Utpal • 0
1
vote
4
replies
365
views
SKAT in R
pvalue skat snp
39 minutes ago by Eliza ▴ 20
0
votes
4
replies
207
views
Problem in retrieving geo data sets
geo
1 day ago by anasjamshed ▴ 120
2
votes
4
replies
376
views
FeatureCounts >edgeR > GO
RNA-SEQ
2 days ago by Pegasus ▴ 80
0
votes
4
replies
736
views
MapSplice2 gives error if the thread count (-p value) is greater than 2
Mapsplice2 fusion_candidates
updated 5 days ago by 127k • written 20 months ago by • 0
0
votes
4
replies
3.6k
views
Genome size estimation using jellyfish
genome jellyfish kmer
updated 4 days ago by 38k • written 5.4 years ago by ▴ 120
1
vote
4
replies
237
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
3 days ago by Agamemnon ▴ 60
3
votes
4
replies
3.5k
views
How Can I Extract All The Read Pairs In A Region From Bam File ?
bam
updated 4 days ago by 38k • written 9.9 years ago by ▴ 150
0
votes
3
replies
182
views
How to deal with the probe id mapping to multiple gene ids?
match microarray affymetrix probe gene
6 hours ago by dare_devil ★ 1.7k
0
votes
3
replies
209
views
using CITE-seq data to cluster single cells
clustering cite-seq k-means 10x
updated 2 days ago by 71k • written 2 days ago by ▴ 40
1
vote
3
replies
195
views
mpileup to sync file
AF samtools selection vcf popoolation
updated 3 days ago by 153k • written 3 days ago by ▴ 20
0
votes
3
replies
656
views
window size
fasta python
updated 4 days ago by 38k • written 16 months ago by ▴ 10
0
votes
3
replies
821
views
Problem to convert genotypes to plink format from bcftools
vcf bcftools ped plink beagle
updated 23 hours ago by ▴ 10 • written 22 months ago by ▴ 10
1
vote
3
replies
485
views
Using Copy Number Alterations detected in other studies for the same tumor cell line
genomes cancer CNV variants CNA
updated 2 days ago by ▴ 100 • written 4 months ago by ▴ 20
1
vote
2
replies
476
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
single-cell ATAC-seq
updated 4 days ago by 38k • written 4 months ago by • 0
1
vote
2
replies
168
views
Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
drug-effect statistical-analysis
2 days ago by E-HR • 0
0
votes
2
replies
1.5k
views
Differences in RNAseq Variant Calling and Allele Specific Expression
RNA-Seq variant calling allele specific expression
updated 2 days ago by • 0 • written 5.1 years ago by ▴ 70
0
votes
2
replies
2.7k
views
demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_strand_adapter --detect_mid_strand_barcodes produce > 90% of unclassified …
demultiplexing guppy
2 days ago by andres.firrincieli 3.2k
2
votes
2
replies
1.4k
views
how are new genes idenitified from analysing genomic data?
next-gen-sequencing
updated 1 day ago by 38k • written 7.5 years ago by ▴ 30
0
votes
2
replies
956
views
Jellyfish histo produces a blank file
genome jellyfish
updated 4 days ago by 38k • written 3.1 years ago by • 0
0
votes
2
replies
3.8k
views
Dssp File Format?
pdb
updated 4 days ago by 38k • written 10.8 years ago by ▴ 30
1
vote
2
replies
1.2k
views
chromosome length .size file
chromosome genome
updated 4 days ago by 38k • written 2.7 years ago by ▴ 50
1
vote
2
replies
194
views
Best way to visualize .paf or .sam alignment to a fasta file
visualization sam fasta paf alignment
updated 1 day ago by 4.6k • written 2 days ago by • 0
0
votes
2
replies
1.4k
views
Predictions of genomic breeding values using haplotypes. Softwares?
SNP
updated 1 day ago by 38k • written 7.6 years ago by • 0
0
votes
2
replies
288
views
LDSC correlation calculate confidence intervals
correlation intervals confidence genetic LDSC
13 hours ago by YL ▴ 10
0
votes
2
replies
233
views
How to limit the use of RAM for clustalo?
Linux Clustalo RAM
2 days ago by animeshizik • 0
0
votes
1
reply
140
views
SKAT iniciation
SKAT
updated 23 hours ago by ★ 1.4k • written 1 day ago by • 0
0
votes
1
reply
107
views
TCGA-BRCA tissue and RNAseq problem
NIH RNAseq GDC TCGA-BRCA
updated 1 hour ago by ▴ 10 • written 17 hours ago by • 0
0
votes
1
reply
107
views
""ERROR：States for individual 0 are zero " when I using GLIMPSE2 for Imputation
PBWT imputation gene GLIMPSE2
updated 19 hours ago by 2.6k • written 23 hours ago by • 0
0
votes
1
reply
185
views
Error parsing strand (?) from GFF line
assembly
updated 4 days ago by ★ 2.9k • written 4 days ago by ▴ 350
0
votes
1
reply
114
views
Plink-association test
association plink case-control covar
updated 23 hours ago by 10k • written 1 day ago by • 0
1
vote
1
reply
244
views
Libraries with different size in the same MiniSeq cartridge
Illumina MiniSeq UMI
updated 4 days ago by 38k • written 11 months ago by • 0
0
votes
1
reply
169
views
SNP ID (rsID) to Chr no. and Position
Annotation
4 days ago by Jewahir • 0
0
votes
1
reply
192
views
doing PBS(population branch statistics) in ANGSD
fst pbs ANGSD
3 days ago by Blessing • 0
3
votes
1
reply
2.3k
views
Noncoding Rna Mapping
non-coding-RNA
updated 4 days ago by 38k • written 9.8 years ago by ▴ 200
0
votes
1
reply
98
views
Gene family classification using RNA-seq data
RNA_seq gene_expression gene_family
updated 19 hours ago by ★ 1.0k • written 20 hours ago by • 0
0
votes
1
reply
142
views
Quality control of Chip-seq data (NRF and PCB)
control library quality PCB Chip-seq NRF
updated 2 days ago by 4.2k • written 3 days ago by • 0
133 results • Page 1 of 3
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Recent Replies
Comment: SKAT in R by Eliza ▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
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