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121,963 results • Page 204 of 2440
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Using STAR aligner to build index of hg38
hg38 STAR alignment RNAseq index
2.0 years ago by Grace • 0
0
votes
2
replies
910
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est clustering
2.0 years ago by Mo ▴ 50
1
vote
2
replies
881
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
0
votes
0
replies
498
views
Compare peaks between clusters in sc-ATAC
Peak-Calling Epigenome scATAC-seq
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 10
1
vote
3
replies
1.4k
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R TCGAbiolinks DESeq2 TCGA
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
0
votes
8
replies
3.2k
views
6 follow
Highly inflated p-values in GWAS by regenie
regenie plink gwas
updated 4 months ago by 12k • written 2.0 years ago by ▴ 40
1
vote
3
replies
1.3k
views
How to find out what adapters to remove after FastQC of RNAseq data?
Trimmomatic FastQC NGS RNA-seq
2.0 years ago by ella • 0
2
votes
5
replies
2.7k
views
Trimmomatic .jar not included anymore?
trimmomatic ubuntu linux
updated 2.0 years ago by ▴ 100 • written 2.0 years ago by ▴ 70
0
votes
1
reply
1.1k
views
News: EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
RNA-seq
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
2
votes
7
replies
2.3k
views
Weirdness in annotation (missing allele frequencies)
allele-frequency gnomad annovar
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
RNA-seq DNA SMARTer
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 80
3
votes
7
replies
2.1k
views
How to check RNAseq support for annotated genes?
gene RNA-seq annotation
updated 2.0 years ago by 56k • written 2.0 years ago by • 0
0
votes
0
replies
771
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
R GEO GEOmetadb
updated 2.0 years ago by 166k • written 2.0 years ago by ▴ 10
1
vote
0
replies
877
views
News: Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow automation pipeline development
2.0 years ago by David Langenberger 11k
2
votes
5
replies
1.8k
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 2.0 years ago by 89k • written 2.0 years ago by ▴ 40
2
votes
2
replies
1.2k
views
Simulate short-read RNA-seq data from long-read RNA-seq data
polyester single-cell simulation short-read long-read
2.0 years ago by rhonddaskl • 0
4
votes
4
replies
1.8k
views
DESeq2 analysis using two featureCounts generated from different studies
RNA-seq DESeq2
2.0 years ago by abedkurdi10 ▴ 190
4
votes
4
replies
1.5k
views
Filtering VCF to divide with equal sizes
bcftools vcf
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 30
0
votes
0
replies
628
views
High pvalues when using clusterProfiler for seurat
clusterProfiler
2.0 years ago by Ahmed ▴ 10
6
votes
3
replies
1.6k
views
kallisto normalized TPM values without bootstraps
tpm cibersort sleuth kallisto RNA-seq
updated 13 months ago by • 0 • written 2.0 years ago by ▴ 30
5
votes
7
replies
2.0k
views
Salmon index not progressing
salmon
updated 2.0 years ago by 56k • written 2.0 years ago by ▴ 160
0
votes
0
replies
1.2k
views
scanpy problem for empty cells
scanpy
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 120
0
votes
0
replies
596
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq nanopore single-cell
2.0 years ago by LauferVA 4.8k
0
votes
1
reply
1.2k
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi cli
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 750
2
votes
1
reply
935
views
News: Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI Codeathon
updated 2.0 years ago by 11k • written 2.0 years ago by ▴ 520
3
votes
4
replies
1.4k
views
Chromosome bias on RNA-Seq differential gene expression analysis
chromosome-bias RNA-seq
2.0 years ago by blz ▴ 40
6
votes
2
replies
1.5k
views
Identifying common DEGs among multiple datasets
R DEG
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by ▴ 20
3
votes
3
replies
2.1k
views
Forum: Importance of Data Structures for Bioinformatics?
data-structures
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
0
votes
2
replies
974
views
How to find positions with higher depth relative to their surroundings
depth python samtools
updated 2.0 years ago by ▴ 160 • written 2.0 years ago by • 0
0
votes
0
replies
650
views
News: Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sequence-analysis sars-cov-2 spike-protein
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
3
votes
2
replies
1.1k
views
How to retrieve LoF and missense variants in WES data?
bcftools variants plink SNPs
updated 2.0 years ago by ▴ 130 • written 2.0 years ago by ▴ 60
0
votes
0
replies
793
views
Recommended workflow for identifying the genomic location and copy-number of an insert with a known sequence from WGS Nanopore fastq files
Nanopore WGS Long-Read
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 70
4
votes
0
replies
996
views
Herald: The Biostar Herald for Wednesday, September 20, 2023
herald
2.0 years ago by Biostar 3.6k
1
vote
4
replies
1.2k
views
I need to retrieve a set of protein and mRNA sequences
Protein mRNA sequences
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
eutils biopython entrez
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
1
vote
2
replies
1.5k
views
GSEA Result Visualization in R
r enrichplot gsea visualization enrichResult
2.0 years ago by Cortney • 0
1
vote
2
replies
1.2k
views
How to separate proteins on the same chain?
pdb protein
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 10
0
votes
2
replies
1.0k
views
how to evaluate SNPs that are regulating same gene expression across multiple tissues
snp GTEx
updated 2.0 years ago by 5.1k • written 2.0 years ago by ▴ 150
3
votes
10
replies
2.6k
views
STAR index not working
STAR RNA-Seq
2.0 years ago by camillab. ▴ 160
1
vote
2
replies
2.0k
views
How to display all top markers in the heatmap by DoHeatmap (Seurat) when there are duplicates of top marker genes for several cell clusters
DoHeatmap Seurat
2.0 years ago by alwayshope ▴ 40
2
votes
3
replies
1.4k
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication apoptosis
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 250
0
votes
1
reply
627
views
Prank checkpoint and restore?
prank alignment
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
0
votes
0
replies
3.0k
views
Job: Research Scientist 5 – Bioinformatics and Computer Biology, Center for Dementia Research (CDR), Nathan Kline Institute for Psychiatric Research
Neuroscience Biostatistics
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
1
vote
1
reply
1.3k
views
gffread outputs empty gtf file
gff gffread gtf
updated 2.0 years ago by ▴ 70 • written 2.0 years ago by • 0
0
votes
13
replies
2.2k
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR Linux
2.0 years ago by Y ▴ 10
5
votes
7
replies
2.6k
views
Elusive syntax error in Snakefile
snakemake
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 30
1
vote
3
replies
1.1k
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools guppy
updated 2.0 years ago by 154k • written 2.0 years ago by • 0
8
votes
10
replies
3.2k
views
Inflated GWAS test statistic after merging multiple batches of genotype dataset imputed differently
genotype imputation gwas
updated 2.0 years ago by 4.8k • written 2.0 years ago by ▴ 20
0
votes
13
replies
2.6k
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn Trinity Transcriptome De-novo-transcriptome-assembly RNA-seq
updated 24 months ago by 45k • written 2.0 years ago by ▴ 70
2
votes
2
replies
1.9k
views
Kraken2 recovering only classified reads
Kraken2 taxonomy classification
2.0 years ago by SushiRoll ▴ 140
121,963 results • Page 204 of 2440
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Comment: Differences between published differential gene expression results and own analy
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Answer: Differences between published differential gene expression results and own analy
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
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Comment: Gene expression equivalent of polygenic risk score ? by Picasa ▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2 by Olivia • 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ? by GouthamAtla 12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin by Ben • 0
write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
That is good confirmation. Bacl to the error message. > I don't know how to fix this, given that I already did the trimming steps. DId yo…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
Honestly, those things shouldn't result in a considerable discrepancy. The largest difference will come from the post-processing & analysi…
Answer: Differences between published differential gene expression results and own analy by Ales ▴ 50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical by Mensur Dlakic ★ 30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy by yura.grabovska ▴ 830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria. by colindaven 8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2 by Olivia • 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
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