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Extracting variations in the gene regions and from 100 bp of gene boundary from multiple VCF files
VCF Variations
updated 3.8 years ago by ★ 1.1k • written 3.8 years ago by ▴ 100
0
votes
0
replies
521
views
Codeml giving different chi2 values when reducing the number of sequences
PAML CODEML
3.8 years ago by Amay ▴ 10
0
votes
0
replies
609
views
VcfSampleCompare - empty output with warnings
VcfSampleCompare empty warnings
3.8 years ago by Michal Nevo ▴ 140
0
votes
0
replies
688
views
PCA on pooled and single individuals
PCA analysis component pooled principal structure samples population
3.8 years ago by javiergandasegui • 0
0
votes
0
replies
603
views
KAAS: Limiting The Genes Associated With a Pathway to a Certain Species
KEGG KAAS pathway metabolic
3.8 years ago by adhamzul ▴ 20
4
votes
5
replies
3.4k
views
6 follow
TopHat error: IOError [errno 2] No such file or directory: '-o'
RNA-Seq rna-seq alignment software error
updated 6.2 years ago by ★ 4.2k • written 6.2 years ago by • 0
0
votes
0
replies
624
views
Extract peptide information from proteomics data
proteomics peptide
3.8 years ago by Gene_MMP8 ▴ 240
0
votes
0
replies
416
views
linking RNA-seq data with GWAS study
ngs
3.8 years ago by hafiz.talhamalik ▴ 350
11
votes
7
replies
15k
views
How to include/keep only the samples in a list in VCF.gz file?
vcf samples bcftools
updated 2.5 years ago by 166k • written 6.9 years ago by ▴ 210
0
votes
0
replies
898
views
What is a good Standardized Beta/standardized regression coefficient in a genetics study?
regression genetics genomics
updated 2.2 years ago by 45k • written 3.8 years ago by ▴ 210
0
votes
0
replies
872
views
Job: Postdoc at Stanford working on mobile health device data from My Heart Counts
ai science device mhealth data
3.8 years ago by hershman ▴ 40
2
votes
2
replies
972
views
Download nucleotide sequence with locus_tag
SEQUENCE LOCUS_TAG NUCLEOTIDE NCBI
3.8 years ago by DJ_MB • 0
6
votes
13
replies
8.0k
views
9 follow
VCF file phasing by SHAPEIT
vcf phasing whole genome shapiet
updated 3.8 years ago by 2.9k • written 6.5 years ago by ★ 1.9k
0
votes
1
reply
1.1k
views
Differential Gene Expression after batch correction with DESC?
DESC scRNAseq batch-effect
updated 9 months ago by 45k • written 3.8 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 3.8 years ago by 15k • written 3.8 years ago by ▴ 40
0
votes
0
replies
557
views
Impute expression from bulk ATAC data
RNA Imputation ATAC
3.8 years ago by kvshamsudheen ▴ 120
1
vote
1
reply
922
views
how to apply DE-kupl in my data for differential expression ?
DE-kupl DE
updated 3.8 years ago by 88k • written 3.8 years ago by ▴ 30
5
votes
7
replies
4.3k
views
Signac CallPeaks from multiple fragment files
Seurat Macs2 Signac
3.7 years ago by LacquerHed ▴ 30
0
votes
0
replies
604
views
PDBePISA calls monomers heteromers, how can one programmatically correct this downstream
PDBe quaternary PISA structure
3.8 years ago by plberry ▴ 30
1
vote
4
replies
1.7k
views
Demultiplexing with Linux
Demultiplexing Linux
updated 3.8 years ago by 21k • written 3.8 years ago by • 0
1
vote
1
reply
1.9k
views
makeblastdb Bus error
bus-error blast
updated 12 months ago by 45k • written 3.8 years ago by ▴ 10
3
votes
10
replies
4.8k
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 2.9 years ago by 152k • written 3.8 years ago by • 0
0
votes
2
replies
2.7k
views
How to change the track background color of IGV
IGV
3.8 years ago by changxu.fan ▴ 80
0
votes
7
replies
1.7k
views
sortsam. picard
picard
updated 3.8 years ago by 45k • written 3.8 years ago by • 0
0
votes
0
replies
622
views
Pathway enrichment for draft gene names
pathway-enrichment
updated 24 months ago by 45k • written 3.8 years ago by ▴ 30
1
vote
2
replies
1.6k
views
HTSeq-count TruSeq RNA Exome Lib Prep
HTseq strandness TruSeqRNAExome nofeatures
3.8 years ago by tdfyoder ▴ 40
0
votes
0
replies
1.6k
views
Job: Science Infrastructure Manager
management infrastructure project Science
3.8 years ago by EMBL Recruitment ▴ 30
1
vote
2
replies
1.1k
views
Accuracy Assembly's contigs
NGS Assembly whole genome Velvet
3.8 years ago by askari.arezou94 ▴ 30
0
votes
0
replies
643
views
Non-symmetric MA-plot (DESeq2)
MA-plot DESeq2
3.8 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 3.8 years ago by ★ 3.0k • written 3.8 years ago by ▴ 30
1
vote
1
reply
912
views
Base recalibration -Java run time error and no sequence dictionary
base GATK NGS recalibration
updated 3.8 years ago by ▴ 840 • written 3.8 years ago by ▴ 70
0
votes
1
reply
828
views
EQTL analysis
sQTL eQTL and
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 50
0
votes
1
reply
807
views
Manhattan Plot in R with 100 non-numeric contigs and chromosomes
contigs chromosomes R Manhattan non-numeric
updated 3.8 years ago by 12k • written 3.8 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 3.8 years ago by ▴ 50
6
votes
9
replies
2.9k
views
Identification of transcription factors from a list of DEGs
DEGs TFs
3.8 years ago by navamikrishna99 ▴ 10
1
vote
0
replies
1.1k
views
Job: Bioinformatician — Biological data and network analysis
network-analysis Biological-data
updated 2.5 years ago by 45k • written 3.8 years ago by ▴ 30
0
votes
1
reply
858
views
how to find interference residue
protein
updated 3.8 years ago by ★ 29k • written 3.8 years ago by ▴ 920
0
votes
0
replies
604
views
Error in reading the annotation files
PyRadiomics Python
3.8 years ago by mxz707 • 0
3
votes
14
replies
4.1k
views
STAR split reads into two strands
rnachip stranded split STAR
3.8 years ago by Alexander • 0
2
votes
7
replies
2.4k
views
fastq file format
fastq NGS
3.8 years ago by Vladimir Leshuk ▴ 50
2
votes
2
replies
1.4k
views
Finding sequence family specific primers using DECIPHER
DECIPHER PCR primer
3.8 years ago by Marcel • 0
0
votes
0
replies
844
views
Best approach to finding correlation between two genes from MAGIC imputed single-cell RNA-seq data
genes MAGIC single-cell corrolation Seurat
3.8 years ago by Stevens ▴ 30
0
votes
5
replies
2.3k
views
How to convert mapping bam file to fastq without loseing the mapping information
bedtools bamtofastq samtools
updated 3.8 years ago by 152k • written 3.8 years ago by • 0
0
votes
0
replies
823
views
ICA - Reconstruction Errors
ICA Omics ML
updated 2.3 years ago by 45k • written 3.8 years ago by • 0
0
votes
3
replies
1.3k
views
Assessing how similar/ different of activated pathways between multiple groups of samples
pathway correlation test hypothesis
updated 3.8 years ago by 4.7k • written 3.8 years ago by ▴ 40
1
vote
2
replies
1.8k
views
Variant Calling Heterozygous Reference Alleles
alignment vcf gatk variant SNP calling
updated 3.8 years ago by 4.7k • written 3.8 years ago by ▴ 10
0
votes
0
replies
869
views
BEDPE file for ENCODE 3D chromatin structure data
BEDPE
3.8 years ago by arsala521 ▴ 60
3
votes
1
reply
6.3k
views
how do I add a title to an Upset plots
Upset plots R
updated 3.8 years ago by 11k • written 3.8 years ago by ▴ 60
0
votes
1
reply
1.3k
views
News: Databricks Runtime for Genomics (Deprecated)
Runtime Databricks Genomics
updated 3.8 years ago by 152k • written 3.8 years ago by ★ 9.6k
5
votes
12
replies
5.7k
views
weird MAplot or volcano plot of DESeq2 diff result
RNA-seq DESeq2
3.8 years ago by shangguandong1996 ▴ 30
121,395 results • Page 583 of 2428
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Answer: Should I perform integration to correct batch effects?
Should I perform integration to correct batch effects?
Answer: Batch correction in TNBC epithelial cells
Answer: When should I NOT apply batch correction for my single-cell RNAseq data?
Answer: Should I perform integration to correct batch effects?
Answer: Batch correction in TNBC epithelial cells
Comment: convert raw counts to TPM
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Comment: Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry by Rob 7.1k
The main issue is that there will be an inherent lack of information (due to the aforementioned 3' bias) in tagged-end data. Nonetheless, …
Comment: Y-axis break in Volcano Plot by antonioggsousa 3.3k
I am not familiar with the package `EnhancedVolcano`, but based on your code, should not you be able to change the y-axis limits through th…
Answer: Clarification of options --keep-dup: all vs. -f FRAG in MACS3 by ATpoint 88k
As per the manual, `FRAG` is specific for scATAC-seq while the other option is generic.
Answer: Should I perform integration to correct batch effects? by antonioggsousa 3.3k
Hi, Please check my previous answer to a similar post/question on this forum: [When should I NOT apply batch correction for my single-cel…
Answer: Batch correction in TNBC epithelial cells by ATpoint 88k
> (1) Is my pipeline correct? Especially re-applying the harmony to the sub-setted the TNBC epithelial cells. You **can** do that. No prob…
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My suggestion is that you consider performing what is commonly referred to as a "delta-delta" contrast. You should be able to find plenty o…
Comment: mgl tool index error by Mahesh • 0
no i am simply drag and drop my pdbqt file in GUI
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At my workplace I created a Singularity image that has most of the C/C++ libraries installed, and R's library path pointing to an image-spe…
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FWIW, I've recently still been running into environment solving issues with conda (even with the incorporated libmamba changes) that mamba …
Comment: How to interpret genomescope to help remove duplicates by mohamadelian1996 • 0
Thank you for helping me out. Other related species have genomes ranging between 400 and 700 Mb so the length given here by genomescope see…
Comment: How to interpret genomescope to help remove duplicates by GenoMax 152k
What is the expected genome size and ploidy for this organism? Can you post the busco results?
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Not a real answer, but it should be pointed out that the only way to learn contrastive filters across modalities (i.e., fluorescence-only e…
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I think this is a borderline bioinformatics question, but I'll still attempt to answer. You won't break the computer by merging all three …
Comment: mgl tool index error by GenoMax 152k
Are you using command line or some sort of GUI? Post the full command if you are doing this on the command line.
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But wait, is the idea with modules that you supply a preloaded config for that module, or that you supply a *path* to a separate config, li…
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