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122,211 results • Page 698 of 2445
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3
votes
5
replies
5.0k
views
Cellranger count command for single end fastq
RNA-Seq sequencing
updated 2.7 years ago by 45k • written 5.0 years ago by ▴ 70
1
vote
1
reply
713
views
How to generate simulated RNA-seq data
RNA-Seq
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
1
vote
0
replies
1.6k
views
germline vs somatic CNV GATK calling
CNV germline somatic GATK WGS
4.7 years ago by cocchi.e89 ▴ 300
0
votes
0
replies
680
views
KEGG mapping of Go ids
RNA-Seq
4.7 years ago by aranyak111 • 0
24
votes
10
replies
10k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 2.7 years ago by 45k • written 5.2 years ago by 13k
0
votes
1
reply
3.0k
views
findOverlapsOfPeaks() of package ChIPpeakAnno in R
R
updated 4.7 years ago by ▴ 10 • written 8.6 years ago by ▴ 550
0
votes
1
reply
2.9k
views
No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
ChIP-Seq annotation
updated 3.2 years ago by 45k • written 10.1 years ago by ▴ 10
0
votes
7
replies
3.3k
views
Cholmod error when using decontX package
R RNA-Seq sequencing
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 30
2
votes
8
replies
1.7k
views
status check missing from multiQC report
RNA-Seq fastqc
4.7 years ago by Lauren • 0
0
votes
0
replies
1.9k
views
Job: Research Associate / Sr. Research Associate
Research
updated 2.3 years ago by 45k • written 4.7 years ago by ▴ 70
2
votes
2
replies
2.0k
views
Difference between read depth, allelic depth and bam readcounts
bam vcf sequencing genotype
updated 4.7 years ago by ▴ 10 • written 4.7 years ago by ▴ 50
1
vote
1
reply
810
views
Summarizing list of Genbank Assembly Accessions
assembly gene genome alignment
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
1
reply
5.1k
views
SNPs density ( count/ per Kb) calculation from VCF file
SNP SNPs density Count/Kb
updated 4.7 years ago by ▴ 10 • written 5.1 years ago by ▴ 220
0
votes
1
reply
1.3k
views
How do I compare two similar PPI networks using Cytoscape?
cytoscape STRING PPI networks
updated 4.7 years ago by ▴ 650 • written 4.7 years ago by ▴ 20
0
votes
0
replies
970
views
Job: Postdoc in Genetic/Epigenetic/Observational Epidemiology (Mount Sinai, NY)
epidemiology genetics neurodevelopment epigenetics
updated 2.3 years ago by 45k • written 4.7 years ago by • 0
1
vote
1
reply
1.1k
views
CWL input files as secondaryFiles JS
CWL input secondaryFiles
updated 4.4 years ago by ★ 1.9k • written 4.7 years ago by ▴ 300
1
vote
3
replies
1.9k
views
different read names in paired-end data
fastq file read name header ABI-Solid
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 270
0
votes
0
replies
768
views
Reference files that can be used for mapping ERVs?
alignment
4.7 years ago by tesic93 ▴ 40
5
votes
4
replies
5.2k
views
6 follow
Gene correlation with single cell data?
RNA-Seq gene
updated 23 months ago by ▴ 10 • written 4.7 years ago by ▴ 50
3
votes
3
replies
3.1k
views
Effect of removing secondary/supplementary alignments from BAM file?
ngs covid-19 SNP
4.7 years ago by cg1440 ▴ 60
12
votes
2
replies
1.9k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 2.7 years ago by 45k • written 4.7 years ago by 13k
0
votes
5
replies
2.6k
views
bam2cfg.pl not able to find statistics : Breakdancer
gen Assembly software error
updated 4.7 years ago by 20 • written 7.2 years ago by ▴ 1000
3
votes
5
replies
4.5k
views
PLINK:Error: Variant '.' is not biallelic. To obtain a full list of merge failures
SNP Assembly genome next-gen
4.7 years ago by williamsbrian5064 ▴ 540
0
votes
0
replies
824
views
Is it possible to impute missing phenotypes (case/control) in Plink .fam files in a GWAS study?
illumina plink GWAS IDAT
4.7 years ago by doughan.albert • 0
0
votes
3
replies
2.1k
views
Uploading text file or any file format in Flexdashboad
R
4.7 years ago by majeedmj.ict ▴ 20
0
votes
0
replies
910
views
How to create link file from NUCmer output
nucmer
4.7 years ago by agata88 ▴ 870
0
votes
1
reply
831
views
How can I convert mouse microarray's Probe IDs into gene names?
R next-gen gene
4.7 years ago by moutazhatem.mh • 0
1
vote
2
replies
992
views
merge paired-end sequencing
SNP merge gatk
4.7 years ago by gubrins ▴ 350
0
votes
4
replies
1.0k
views
Error when running Rscript under Ubuntu
R
4.7 years ago by Evy_00 • 0
2
votes
3
replies
1.5k
views
extract region.txt from bam file
alignment Assembly rna-seq
4.7 years ago by madiha_shabbir46 ▴ 10
0
votes
0
replies
1.2k
views
adjust size of png images in a rasterGrob object
rasterGrob PNG Rmarkdown layout
4.7 years ago by Assa Yeroslaviz ★ 1.9k
2
votes
2
replies
1.3k
views
Mapping after WGS show a parabel form
WGS mapping SNP CNV
updated 6 months ago by ▴ 20 • written 4.7 years ago by ★ 1.9k
3
votes
1
reply
1.1k
views
Can someone recommend a bioinformatics book that is programming oriented?
python
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by • 0
8
votes
5
replies
5.5k
views
Can someone explain in detail the meaning of a gseaplot in GSEA
gseaplot
updated 4.7 years ago by ▴ 270 • written 5.6 years ago by ▴ 410
0
votes
1
reply
2.6k
views
Na (No Value) In Chromosome In Output Snp Test
chromosome
updated 4.7 years ago by • 0 • written 12.0 years ago by • 0
3
votes
2
replies
1.6k
views
qualimap2 mean mapping quality
alignment
updated 4.2 years ago by ▴ 10 • written 4.7 years ago by ▴ 30
11
votes
4
replies
1.8k
views
How to determine % similarity between genomes?
mauve mugsy genome-alignment
updated 2.2 years ago by 45k • written 4.7 years ago by ▴ 180
0
votes
0
replies
817
views
Augustus training with partial transcriptome?
augustus maker maker2 annotation
4.7 years ago by DNAlias ▴ 40
3
votes
3
replies
1.5k
views
Help regarding RNAseq data analysis.
RNA-Seq alignment next-gen
updated 4.7 years ago by 20 • written 6.4 years ago by ▴ 20
2
votes
3
replies
1.5k
views
How to export STAR alignment output files
RNA-Seq
updated 4.7 years ago by ★ 1.5k • written 4.7 years ago by ▴ 10
0
votes
0
replies
801
views
What do the + and - mean in KEGG Ortholog combinations under a particular Module?
kegg database module ortholog identifiers
4.7 years ago by O.rka ▴ 750
4
votes
3
replies
4.4k
views
How to get a mapping between KEGG module and KEGG orthologs?
KEGG Annotation Ortholog Module
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 750
0
votes
0
replies
956
views
RNA-Seq Deconvolution algorithm for FACS pre-sorted cells
RNA-Seq deconvolution TIMER
4.7 years ago by Stefan • 0
0
votes
2
replies
757
views
How to identify the reads from diffient seq-data is from the same gene?
rna-seq
updated 4.7 years ago by 13k • written 4.7 years ago by • 0
2
votes
2
replies
3.1k
views
Confused about TSS coordinates
ChIP-Seq
updated 4.7 years ago by ▴ 20 • written 6.4 years ago by ▴ 70
0
votes
0
replies
968
views
Covariates on non-phenotype fam file?
plink genotyping covariates
4.7 years ago by kstafford32 • 0
0
votes
2
replies
1.3k
views
I need to visualize the correlation in better way
multi-omics
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 80
0
votes
1
reply
718
views
RNA Seq Classification
RNA-Seq
4.7 years ago by mosquitoking • 0
0
votes
0
replies
568
views
deduce haplotypes from genotypes
clarks algorithm
updated 4.7 years ago by 20 • written 4.8 years ago by • 0
1
vote
2
replies
1.2k
views
How to make co expression analysis with normalised count rna seq data
R rna-seq
updated 4.7 years ago by ▴ 940 • written 4.7 years ago by ▴ 30
122,211 results • Page 698 of 2445
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Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 130
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
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