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Job: Postdoc at Stanford working on mobile health device data from My Heart Counts
ai science device mhealth data
3.9 years ago by hershman ▴ 40
2
votes
2
replies
996
views
Download nucleotide sequence with locus_tag
SEQUENCE LOCUS_TAG NUCLEOTIDE NCBI
3.9 years ago by DJ_MB • 0
6
votes
13
replies
8.1k
views
9 follow
VCF file phasing by SHAPEIT
vcf phasing whole genome shapiet
updated 3.9 years ago by 2.9k • written 6.6 years ago by ★ 1.9k
0
votes
1
reply
1.2k
views
Differential Gene Expression after batch correction with DESC?
DESC scRNAseq batch-effect
updated 10 months ago by 45k • written 3.9 years ago by ▴ 80
2
votes
3
replies
1.8k
views
how htseq-count counts unstranded RNA-seq data
htseq-count RNA-seq stranded
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 40
0
votes
0
replies
567
views
Impute expression from bulk ATAC data
RNA Imputation ATAC
3.9 years ago by kvshamsudheen ▴ 120
1
vote
1
reply
943
views
how to apply DE-kupl in my data for differential expression ?
DE-kupl DE
updated 3.9 years ago by 88k • written 3.9 years ago by ▴ 30
5
votes
7
replies
4.3k
views
Signac CallPeaks from multiple fragment files
Seurat Macs2 Signac
3.8 years ago by LacquerHed ▴ 30
0
votes
0
replies
611
views
PDBePISA calls monomers heteromers, how can one programmatically correct this downstream
PDBe quaternary PISA structure
3.9 years ago by plberry ▴ 30
1
vote
4
replies
1.7k
views
Demultiplexing with Linux
Demultiplexing Linux
updated 3.9 years ago by 21k • written 3.9 years ago by • 0
1
vote
1
reply
1.9k
views
makeblastdb Bus error
bus-error blast
updated 12 months ago by 45k • written 3.9 years ago by ▴ 10
3
votes
10
replies
4.9k
views
6 follow
How do I match my transcript ID's from NCBI to the corresponding gene ID's to enable tximport into R?
Salmon tximport RNA-Seq R
updated 3.0 years ago by 152k • written 3.9 years ago by • 0
0
votes
2
replies
2.8k
views
How to change the track background color of IGV
IGV
3.9 years ago by changxu.fan ▴ 80
0
votes
7
replies
1.7k
views
sortsam. picard
picard
updated 3.9 years ago by 45k • written 3.9 years ago by • 0
0
votes
0
replies
625
views
Pathway enrichment for draft gene names
pathway-enrichment
updated 2.0 years ago by 45k • written 3.9 years ago by ▴ 30
1
vote
2
replies
1.6k
views
HTSeq-count TruSeq RNA Exome Lib Prep
HTseq strandness TruSeqRNAExome nofeatures
3.9 years ago by tdfyoder ▴ 40
0
votes
0
replies
1.6k
views
Job: Science Infrastructure Manager
management infrastructure project Science
3.9 years ago by EMBL Recruitment ▴ 30
1
vote
2
replies
1.1k
views
Accuracy Assembly's contigs
NGS Assembly whole genome Velvet
3.9 years ago by askari.arezou94 ▴ 30
0
votes
0
replies
664
views
Non-symmetric MA-plot (DESeq2)
MA-plot DESeq2
3.9 years ago by mdidish • 0
4
votes
7
replies
2.7k
views
Inferring CNVs from BAM files with SAMTools depth
samtools bam wes wgs cnv
updated 3.9 years ago by ★ 3.0k • written 3.9 years ago by ▴ 30
1
vote
1
reply
920
views
Base recalibration -Java run time error and no sequence dictionary
base GATK NGS recalibration
updated 3.9 years ago by ▴ 840 • written 3.9 years ago by ▴ 70
0
votes
1
reply
844
views
EQTL analysis
sQTL eQTL and
updated 3.9 years ago by ★ 3.3k • written 3.9 years ago by ▴ 50
0
votes
1
reply
814
views
Manhattan Plot in R with 100 non-numeric contigs and chromosomes
contigs chromosomes R Manhattan non-numeric
updated 3.9 years ago by 12k • written 3.9 years ago by ▴ 140
1
vote
2
replies
3.1k
views
Filter on Allele Balance using BCFTools
bcftools allele filter balance
updated 3.6 years ago by ★ 9.6k • written 3.9 years ago by ▴ 50
6
votes
9
replies
2.9k
views
Identification of transcription factors from a list of DEGs
DEGs TFs
3.9 years ago by navamikrishna99 ▴ 10
1
vote
0
replies
1.1k
views
Job: Bioinformatician — Biological data and network analysis
network-analysis Biological-data
updated 2.6 years ago by 45k • written 3.9 years ago by ▴ 30
0
votes
1
reply
881
views
how to find interference residue
protein
updated 3.9 years ago by ★ 29k • written 3.9 years ago by ▴ 920
0
votes
0
replies
613
views
Error in reading the annotation files
PyRadiomics Python
3.9 years ago by mxz707 • 0
3
votes
14
replies
4.1k
views
STAR split reads into two strands
rnachip stranded split STAR
3.9 years ago by Alexander • 0
2
votes
7
replies
2.5k
views
fastq file format
fastq NGS
3.9 years ago by Vladimir Leshuk ▴ 50
2
votes
2
replies
1.4k
views
Finding sequence family specific primers using DECIPHER
DECIPHER PCR primer
3.9 years ago by Marcel • 0
0
votes
0
replies
859
views
Best approach to finding correlation between two genes from MAGIC imputed single-cell RNA-seq data
genes MAGIC single-cell corrolation Seurat
3.9 years ago by Stevens ▴ 30
0
votes
5
replies
2.4k
views
How to convert mapping bam file to fastq without loseing the mapping information
bedtools bamtofastq samtools
updated 3.9 years ago by 152k • written 3.9 years ago by • 0
0
votes
0
replies
838
views
ICA - Reconstruction Errors
ICA Omics ML
updated 2.3 years ago by 45k • written 3.9 years ago by • 0
0
votes
3
replies
1.4k
views
Assessing how similar/ different of activated pathways between multiple groups of samples
pathway correlation test hypothesis
updated 3.9 years ago by 4.8k • written 3.9 years ago by ▴ 40
1
vote
2
replies
1.8k
views
Variant Calling Heterozygous Reference Alleles
alignment vcf gatk variant SNP calling
updated 3.9 years ago by 4.8k • written 3.9 years ago by ▴ 10
0
votes
0
replies
888
views
BEDPE file for ENCODE 3D chromatin structure data
BEDPE
3.9 years ago by arsala521 ▴ 60
3
votes
1
reply
6.4k
views
how do I add a title to an Upset plots
Upset plots R
updated 3.9 years ago by 11k • written 3.9 years ago by ▴ 60
0
votes
1
reply
1.3k
views
News: Databricks Runtime for Genomics (Deprecated)
Runtime Databricks Genomics
updated 3.9 years ago by 152k • written 3.9 years ago by ★ 9.6k
5
votes
12
replies
5.8k
views
weird MAplot or volcano plot of DESeq2 diff result
RNA-seq DESeq2
3.9 years ago by shangguandong1996 ▴ 30
1
vote
6
replies
1.6k
views
extraction of last 400 nucleotide from fastq file using python
Python fastq
updated 3.9 years ago by 45k • written 3.9 years ago by ▴ 80
2
votes
4
replies
1.4k
views
How to remove reads mapped to both plasmid and chromosome from the .sam file?
SAM-file NGS small-RNA
2.8 years ago by Vasiliy Krestov ▴ 30
1
vote
2
replies
1.5k
views
MCPcounter LibreSSL SSL_connect: SSL_ERROR_SYSCALL in connection to raw.githubusercontent.com:443
MCPcounter
3.9 years ago by Binghong ▴ 20
3
votes
2
replies
1.4k
views
problem with Trinity command run in denovo transcriptome assembly
analysis trinity transcriptome denovo
3.9 years ago by Aliviya • 0
1
vote
6
replies
2.0k
views
HISAT2: Question regarding providing file path to indexed genome folder
hisat2 alignment indexed
updated 3.9 years ago by 88k • written 3.9 years ago by ▴ 30
0
votes
1
reply
879
views
Metawrap pipeline doesn't detect samples
metawrap
3.9 years ago by arshad1292 ▴ 110
1
vote
2
replies
993
views
Spliiting the bam files into separate samples ,tophat2
plant_sequence fraser rna splicing tophat2 data sequencing
3.9 years ago by Dixi • 0
0
votes
5
replies
2.6k
views
How to adjust p value after Wilcoxon rank sum test?
p-value TADs statistics Hi-C
updated 3.9 years ago by 56k • written 3.9 years ago by • 0
0
votes
0
replies
648
views
ProcessMethylation450Data function of TCGA-Assembler causing subscript out of bound error
of ProcessMethylation450Data out subscript bounds
3.9 years ago by Sheetal • 0
1
vote
3
replies
1.6k
views
smartPCA: problem with .evec file
smartpca
updated 2.3 years ago by 45k • written 3.9 years ago by ▴ 20
121,533 results • Page 586 of 2431
Recent Votes
Comment: Mitochondrial annotation tool for algae
Answer: Picking optimal resolution for single cell in seurat pipeline
A: Tools To Identify Compound Heterozygous Variants?
Answer: What purposes can TPM values be used for?
Answer: What purposes can TPM values be used for?
Comment: Trouble getting representatives from clustered_nr database
A: Difference between primary nad capture targets
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Recent Replies
Comment: Mitochondrial annotation tool for algae by Juke34 9.2k
The last version of it is here => [https://juke34.github.io/awesome-genome-annotation/][1] [1]: https://juke34.github.io/awesome-genome…
Comment: Identifying gene outliers in a genome using composition analysis. by GenoMax 152k
> I want to separate the bacterial sequences from the plant sequences using sequence composition analyses. Use `CheckM` --> https://www.b…
Comment: Mapping to a template sequece by GenoMax 152k
> with two regions of approximately 20 bp each that contain variable bases Where are these located in the reference? `bwa-mem2` aligns r…
Comment: Problem with Mirdeep2 and Randfold output by GenoMax 152k
Original poster solved their problem by using the solution they noted below. Have you tried it?
Comment: Mitochondrial annotation tool for algae by GenoMax 152k
@juke34 has a list of tools here that you can take a look through: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/anno…
Comment: quality control for 16s metagenome reads by GenoMax 152k
> I have 16S metagenomic reads that are of poor quality. If true, not much you can do about changing that. Instead of getting stuck on Fas…
Comment: Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger mult by GenoMax 152k
You will need to drop the other assays besides GEX to get the that file then or find an alternate solution.
Comment: Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger mult by tlallihuacan • 0
Thanks @genomax I did that the next day I saw I didn't get the answer here, I am coming back now. This is what 10x answered: "Thank yo…
Answer: quality control for 16s metagenome reads by Asaf 10k
I would have: 1. Discussed it with the sequencing service provider, there might be a problem with the machine (I've never seen such a pat…
Comment: PCA interpretation by ATpoint 88k
I do not recommend exploring noise-prone assays like ChIP-seq in a "blind" matter like this, using just the BAM files as input. Do proper p…
Comment: Loss of strandedness in the Illumina Strandedness Total RNA protocol by ATpoint 88k
No, I've never seen this before other than people used different kits than anticipated, or things were done wrong in the lab. Use an indepe…
Answer: Loss of strandedness in the Illumina Strandedness Total RNA protocol by Gordon Smyth ★ 8.2k
Running featureCounts would confirm for certain whether the RNA-seq is stranded or not, and also whether it appears usable or not. See: htt…
Comment: Which Reference Hg38 or T2T?? Both?? by Jon • 0
Those were BLAST results using the default NCBI Core_nt database, which apparently includes human reads sequenced nearly 20-25 years ago, s…
Comment: How to rank genes for GSEA using edgeR-LRT results ? by Gordon Smyth ★ 8.2k
Yes. That is a quasi t-statistic.
Comment: Problem with Mirdeep2 and Randfold output by Raquel • 0
Hi! I'm having the same problem. Did you solve it? Thank you, Best
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