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523
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bowtie2 doesn't align reads concordantly within the distance given
bowtie2
23 months ago by tnminh89 ▴ 10
1
vote
4
replies
1.3k
views
will using samtools merge to multiple bam files also remove the redundancy ?
bamtools samtools
updated 23 months ago by 154k • written 23 months ago by ▴ 10
1
vote
3
replies
1.8k
views
FPKM values for DE analysis - Why?
fpkm rna-seq
updated 23 months ago by ★ 4.7k • written 23 months ago by • 0
1
vote
10
replies
2.4k
views
Xenocell - Error in classify reads
Xenocell PDX scRNAseq singularity-container
updated 23 months ago by 45k • written 2.6 years ago by • 0
1
vote
6
replies
1.5k
views
error in Fastq
everyone
updated 23 months ago by 45k • written 23 months ago by • 0
0
votes
0
replies
489
views
Does chromosome order matter when combining individual primary assembly files?
ensembl genome rna-seq
23 months ago by iahuja • 0
0
votes
1
reply
778
views
metagenomics analysis
shutgun metagenomics
updated 23 months ago by ★ 4.0k • written 23 months ago by • 0
0
votes
1
reply
962
views
XenoCell fq.gz output files
scRNA xenocell PDX
updated 23 months ago by 45k • written 2.6 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Apt-format-result provides .map file (for exporting plink format) with all null values except affymetrix id column
APT plink
updated 23 months ago by 45k • written 23 months ago by ▴ 10
0
votes
0
replies
1.3k
views
Job: Staff Scientist (AC-TAP) in Database Development at Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of…
Django JavaScript python Flask
updated 23 months ago by 45k • written 23 months ago by ▴ 80
0
votes
2
replies
834
views
Fisher exact test on different gene sets
fisher-test
updated 23 months ago by 45k • written 23 months ago by • 0
1
vote
3
replies
1.3k
views
No valid chromosomes found! on Michigan Imputation Server
michigan-imputation-server
updated 23 months ago by ★ 3.1k • written 23 months ago by ▴ 110
11
votes
6
replies
1.6k
views
Medical genetics server for a developing country
server
updated 23 months ago by ★ 3.5k • written 23 months ago by ★ 3.0k
2
votes
1
reply
1.5k
views
Filtering for primary and secondary reads using sam flags (0 properly paired reads in alignment step)
freebayes samtools samflags sam paired-end
updated 23 months ago by ▴ 390 • written 23 months ago by ▴ 10
4
votes
6
replies
1.8k
views
OMA in AWS cloud
OMA AWS
updated 23 months ago by ★ 1.1k • written 2.0 years ago by ▴ 10
2
votes
3
replies
1.2k
views
How do I add sample annotations to this data?
R data visualization ggplot2
updated 23 months ago by ★ 3.1k • written 23 months ago by • 0
1
vote
3
replies
1.0k
views
cell ranger count
scRNA-seq cellranger single-cell
updated 23 months ago by 89k • written 23 months ago by ▴ 10
0
votes
1
reply
555
views
kover directory, run the installer
kover install
updated 23 months ago by 166k • written 23 months ago by • 0
0
votes
0
replies
578
views
RAP.ID to KEGG ID converter
RAP.ID KEGG RStudio
updated 23 months ago by 45k • written 23 months ago by • 0
3
votes
3
replies
1.1k
views
Need Control Gene Count Files
R RNA-Seq TCGA
updated 23 months ago by ▴ 20 • written 23 months ago by ▴ 30
0
votes
0
replies
534
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
23 months ago by meenae • 0
0
votes
0
replies
477
views
Normalisation of PLINK/VCF files?
plink
23 months ago by optimistsso4co3 ▴ 140
0
votes
0
replies
805
views
How to convert dataframe properly to anndata?
single-cell python anndata
updated 18 months ago by 45k • written 23 months ago by ▴ 160
0
votes
4
replies
1.7k
views
Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated
RNAseq DEseq time-course microarray
23 months ago by Shero ▴ 10
1
vote
2
replies
1.2k
views
How to plot two categorical variables in ggridges?
R ggridges ggplot2
updated 23 months ago by 4.2k • written 23 months ago by ▴ 60
3
votes
0
replies
919
views
Job: Bioinformatician, Funga, Austin Texas USA
eDNA
updated 23 months ago by 8.0k • written 23 months ago by ▴ 30
1
vote
1
reply
703
views
Intenger encoding versus one-hot encoding for chromosome as a predictor in a neural network
neural-network predictor chromosome
updated 23 months ago by 45k • written 23 months ago by ▴ 30
17
votes
20
replies
3.9k
views
What is the best way to compute genetic distances between FASTQ files?
genetic-distance fastq
updated 23 months ago by 154k • written 23 months ago by ▴ 10
0
votes
0
replies
496
views
Bcftools Consensus - Choose Random Allele for Heterozygous Sites
bcftools
updated 23 months ago by 45k • written 23 months ago by ▴ 20
1
vote
2
replies
1.1k
views
should I use normalized counts or transformed of normalized counts for RNA-seq association analysis?
methylation DESeq RNA-Seq
23 months ago by Alewa ▴ 190
1
vote
5
replies
1.4k
views
how to convert beta effect size of SNP to a statistical value to be compared across tissues
beta-effect statistics SNP multi-variate
updated 23 months ago by 5.1k • written 23 months ago by ▴ 150
17
votes
12
replies
19k
views
10 follow
Converting from BED to SAF/GFF
bed gff saf featureCount
updated 23 months ago by • 0 • written 8.8 years ago by ▴ 60
3
votes
9
replies
1.6k
views
STARsolo seg fault without readMapNumber flag
STAR RNA-seq STARsolo Velocyto
updated 23 months ago by 45k • written 23 months ago by ▴ 420
0
votes
0
replies
766
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python anndata atac-seq
updated 18 months ago by 45k • written 23 months ago by ▴ 160
1
vote
1
reply
837
views
Calculating E-value from Exonerate and choosing minimum percentage identity.
Exonerate E-value
updated 23 months ago by 27k • written 23 months ago by • 0
0
votes
9
replies
2.4k
views
fragments file generation via Sinto from CellRanger output
scATAC alignment scRNA Sinto 10x
23 months ago by ntsopoul ▴ 60
0
votes
0
replies
568
views
Errors in Functional Enrichment Analysis with Clusterprofiler
GSCA R GO Enrichment Clusterprofiler
23 months ago by Tanjim • 0
0
votes
0
replies
444
views
Vg tools - variant length
vg
23 months ago by zuzka.halenkova • 0
1
vote
0
replies
886
views
Job: Assistant Professor of Computational Biology - Georgia College & State University
computational-biology PUI tenure-track
updated 23 months ago by 45k • written 23 months ago by ▴ 10
5
votes
7
replies
3.6k
views
download files from NCBI SRA
NCBI AWS SRA
updated 23 months ago by ★ 4.3k • written 23 months ago by ▴ 10
0
votes
1
reply
665
views
Percentage of samples covered per region in IGV
bam coverage igv
updated 23 months ago by ★ 4.3k • written 23 months ago by ▴ 20
0
votes
0
replies
518
views
Mapping .fna reference genome to itself in order to include it as an outgroup
fasta bowtie2 mapping
23 months ago by Michal • 0
1
vote
0
replies
658
views
Input data matrix from Seurat toolkit analysis for RNA velocity analysis using scvelo
seurat velocity scvelo scrnaseq
23 months ago by sarahmanderni ▴ 130
3
votes
2
replies
1.6k
views
Small RNA sequencing using Illumina 2 channel SBS: how to deal with Gs?
SBS small RNA
updated 23 months ago by ▴ 120 • written 23 months ago by ▴ 60
0
votes
1
reply
827
views
How to correct for known and surrogate variables in DESeq2?
sva DEseq2 limma batch-effect
updated 19 months ago by ▴ 20 • written 23 months ago by • 0
0
votes
3
replies
1.2k
views
unbiased clustering of these top 50 genes in seurat
seurat heatmap
updated 23 months ago by 45k • written 23 months ago by ▴ 10
0
votes
0
replies
504
views
RRBS Data analysis with Methylkit
methylation rrbs methylkit r
23 months ago by 296cd367 • 0
1
vote
3
replies
1.1k
views
Complexity curve for PE fastq files
complexity fastq
updated 23 months ago by 20k • written 23 months ago by ▴ 650
11
votes
7
replies
14k
views
7 follow
Association Analysis with Plink error
SNP plink plink2 association
updated 6 months ago by • 0 • written 9.5 years ago by ▴ 60
2
votes
1
reply
815
views
Where can I find links to scientific articles connected to trials referenced in the AACT
studies AACT
updated 23 months ago by 23k • written 23 months ago by ▴ 10
121,961 results • Page 191 of 2440
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sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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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…
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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…
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When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
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Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
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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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On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
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Yes but the problem is that biological knowledge is never fully encompasing. While I can say that a cell expressing CD45 alongside astrocyt…
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Human genome, ideally hg38
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Hello, I am wondering if you got access to the software or not. I am looking to use Newbler for my research and I contacted Roche too but t…
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
> I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST. I assume you did the above to generate the transcriptome,…
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Got it https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-inclusion-list-formerly-barcode-whitelist
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