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122,202 results • Page 668 of 2445
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two allele frequency
allele position BCFTOOLS
updated 4.6 years ago by 14k • written 4.6 years ago by ▴ 110
0
votes
0
replies
654
views
How to average DESeq2’s median of ratios from replications
Deseq2
4.6 years ago by yosapol.harn • 0
0
votes
3
replies
1.7k
views
Cellular deconvolution intuition
deconvolution
4.6 years ago by Aspire ▴ 390
0
votes
1
reply
643
views
how to use python to only read sequences from fasta files
sequencing python genome fasta
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 10
0
votes
0
replies
764
views
Freebayes - too many variants produced on WES sample
Freebayes
4.6 years ago by esimonova.me ▴ 30
0
votes
1
reply
1.0k
views
Bash Script for a specific SNP
SARS-CoV-2 BASH SNPS
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
3
replies
1.3k
views
RefSeq assession IDs
RefSeq Gene
4.6 years ago by chaochao ▴ 20
0
votes
0
replies
917
views
how to downlaod parkinson's disease GWAS summary statistics file
GWAS
4.6 years ago by BenHu • 0
0
votes
2
replies
2.1k
views
Error while plotting heatmap
heatmap RStudio
4.6 years ago by mrinsmrids • 0
1
vote
1
reply
696
views
Differential expression analysis using SCAN data
differential-expression
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
1
reply
5.0k
views
simplify function on enricher output of ClusterProfiler
clusterProfiler
updated 4.6 years ago by ▴ 20 • written 6.7 years ago by • 0
0
votes
1
reply
1.0k
views
Conflict result between RNA-seq and Western-Blot
RNAseq protein
updated 4.6 years ago by ★ 3.1k • written 4.6 years ago by ★ 9.6k
0
votes
0
replies
859
views
Why do I keep encountering the following errors whenever I run the naccess program to calculate the interface area of a protein with multiple chains?
Naccess Interface-area PDB PPI
4.6 years ago by Cm • 0
0
votes
0
replies
697
views
Single Factor Design and Dispersion and BCV
bcv dispersion edegr
4.6 years ago by plewis8 • 0
0
votes
0
replies
752
views
clarification about WGA (Whole genome Amplification)
sample library NGS
4.6 years ago by Ruolin Liu • 0
1
vote
7
replies
3.5k
views
many intronic reads and no features counts in 3' RNA-seq sequencing
RNA-Seq
updated 4.6 years ago by ▴ 80 • written 5.8 years ago by ▴ 10
5
votes
6
replies
3.1k
views
Error in library(preproc) : there is no package called ‘preproc’
metaOmics R Packages Rstudio
4.6 years ago by xxxxxxxx ▴ 20
0
votes
3
replies
3.2k
views
Allele Specific Expression (ASE) from RNA seq data
AlleleSpecificExprssion ASEReadCounter RNAseq
updated 4.6 years ago by ▴ 730 • written 4.6 years ago by ▴ 140
0
votes
1
reply
1.7k
views
To construct the Venn diagram from Roary
roary pangenome venn
updated 4.6 years ago by • 0 • written 4.7 years ago by • 0
0
votes
0
replies
732
views
Simulated data or pseudoreplicatesreported in papers
pseudoreplicates SNPs INDELs
4.6 years ago by esimonova.me ▴ 30
0
votes
0
replies
1.9k
views
Job: Research Scientist at Lausanne, Swiss Institute of Bioinformatics
nash omics SIB research
4.6 years ago by Rishika • 0
0
votes
2
replies
1.0k
views
Gene ontology analysis
enrichment methylation gene_identifier
4.5 years ago by Kajol • 0
0
votes
0
replies
2.0k
views
grouping in EdgeR
EdgeR RNA-SEQ
4.6 years ago by BDK_compbio ▴ 140
0
votes
2
replies
1.3k
views
DESEQ2
featurecount DeSeq2
4.6 years ago by rheab1230 ▴ 150
0
votes
1
reply
813
views
What type of statistical study can I can conduct based on data obtained
r statistics
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 10
0
votes
0
replies
903
views
Job: Positions at the Penn Epigenetics Institute
computational-biology epigenetics
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
2
votes
3
replies
7.9k
views
10x scRNA-Seq Multiplet Calculations
doublet multiplet 10x scRNA-Seq QC
4.5 years ago by Charles Warden 8.3k
0
votes
4
replies
1.4k
views
Transcription factor
RNA-seq analysis
4.6 years ago by rheab1230 ▴ 150
0
votes
0
replies
978
views
Job: Postdoc position in computational population genetics
populationgenetics ancientdna postdoc
4.6 years ago by Gabriel R. ★ 2.9k
2
votes
4
replies
3.0k
views
bedGraphToBigWig
Seq ChIP
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 170
0
votes
0
replies
1.1k
views
snpEff gives warning: INFO_REALIGN_3_PRIME, what does it mean?
annotation vep snpeff
4.6 years ago by boxate1618 ▴ 60
1
vote
1
reply
1.5k
views
scRNA-Seq GEX 5' v1.0 High Cell Count with Low Gene Count
10x scRNA-seq downsampling
4.6 years ago by tdfyoder ▴ 40
1
vote
5
replies
2.3k
views
Memory Error
R Memory MOFA
updated 4.6 years ago by ★ 2.9k • written 4.6 years ago by ▴ 110
3
votes
5
replies
2.3k
views
metaOmics Installation issues in windows 4.0.5 using R
metaOmics R meta-analysis R-studio
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 20
0
votes
1
reply
1.4k
views
How to find single copy genes from OrthoFinder output
singlecopygenes Orthofinder
updated 4.6 years ago by ★ 2.9k • written 4.6 years ago by • 0
3
votes
3
replies
1.8k
views
Remove unknown batch effect in microarrays data
ruv batch microarray sva removebatcheffect
4.6 years ago by antonio.dos.hermanas ▴ 20
2
votes
2
replies
1.2k
views
MetaOmics installation issues in R version 4.0.5
R MetaOmics R-studio Metadata-analysis
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 20
0
votes
2
replies
2.0k
views
How do I do pathview analysis to get Kegg pathways with DEG lists
rna-sequencing Pathview
4.6 years ago by ashwing.kofficial ▴ 10
0
votes
5
replies
2.3k
views
Possible to merge three plink bim, bed and fam files?
bmerge Plink1.9
updated 4.6 years ago by 2.9k • written 4.6 years ago by ▴ 70
1
vote
1
reply
1.1k
views
Seqrecord object to only a single line sequence (without ID)
SeqIO biopython python
updated 2.5 years ago by 45k • written 4.6 years ago by • 0
0
votes
3
replies
2.0k
views
GATK VariantFiltration error "-12.5 is not a recognized option"
GATK VariantFiltration SelectVariant
4.6 years ago by chloe.girard • 0
4
votes
5
replies
4.7k
views
Star alingment, Salmon quantification
SALMON STAR STAR-SALMON
4.5 years ago by lidiaryabova • 0
0
votes
1
reply
760
views
Matlib Runtime Libraries
JRE Quantisnp
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
5
votes
7
replies
4.8k
views
how is seurat computing logcounts?
singlecellexperiment single-cell seurat
4.6 years ago by tbg ▴ 120
2
votes
0
replies
880
views
Admixture Plot Problem
Admixture
4.6 years ago by mscpythonstudy ▴ 20
0
votes
0
replies
726
views
BioPython Resriction package output formatting
Biopython
4.6 years ago by daewowo ▴ 80
0
votes
0
replies
1.4k
views
Adding Principal components as covariates in GWAS studies
PCA SNP GWAS GEMMA
4.6 years ago by anikcropscience ▴ 270
0
votes
4
replies
2.9k
views
trim_galore error: Cutadapt terminated with exit signal: '256'
RNA-seq cutadapt chip-seq sequencing trimgalore
4.6 years ago by szp770 ▴ 10
4
votes
2
replies
7.5k
views
BiocLite installation issues in R version 4.0.5
R BiocLite Bioconductor BiocManager R-studio
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 20
0
votes
0
replies
589
views
Forum: How is is is xxx?
sum-of-airs
4.5 years ago by aa • 0
122,202 results • Page 668 of 2445
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A: Regarding Microarray Platforms
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
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Recent Replies
Comment: 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 • 0
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!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
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