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931 results • Page 7 of 19
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3
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232
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Software to separate reads from different individuals
software development nanopore
updated 10 days ago by 142k • written 10 days ago by ▴ 20
0
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3
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212
views
STAR aligner error
RNA-seq STAR slurm
updated 23 hours ago by 43k • written 1 day ago by ▴ 30
3
votes
3
replies
743
views
KissDE and batch effect
kissDE kissplice
17 days ago by david.b.rombaut ▴ 10
5
votes
3
replies
740
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 20 days ago by • 0 • written 9 months ago by ▴ 310
1
vote
3
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319
views
some error in building kraken2 database
metagenome kraken2
15 days ago by Art1ess • 0
1
vote
3
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431
views
Limma compare between 3 conditions vs 2 conditions
Limma
updated 22 days ago by ★ 7.1k • written 6 weeks ago by ▴ 280
0
votes
3
replies
424
views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
updated 16 days ago by 6.4k • written 24 days ago by • 0
1
vote
3
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500
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix regression
updated 23 days ago by 3.9k • written 24 days ago by ▴ 120
7
votes
3
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4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 22 days ago by 43k • written 5.1 years ago by ▴ 100
2
votes
3
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820
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 5 days ago by • 0 • written 7 months ago by • 0
0
votes
3
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358
views
10x GEX and ADT data analysis in Seurat
Seurat scRNA-seq ADT Cite-seq GEX
updated 26 days ago by 82k • written 28 days ago by • 0
1
vote
3
replies
873
views
add INFO tag to vcf with bcftools
bcftools vcf
updated 23 days ago by 43k • written 2.0 years ago by ▴ 230
1
vote
3
replies
416
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology metagenomics database enzymes genomics
updated 10 days ago by ★ 27k • written 12 days ago by ▴ 720
3
votes
3
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2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 14 days ago by • 0 • written 22 months ago by ▴ 180
4
votes
3
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1.0k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 8 hours ago by 161k • written 9 hours ago by ★ 1.2k
2
votes
3
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942
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R RNA-Seq DE batch-effect GTEx
updated 24 days ago by 43k • written 4.1 years ago by ▴ 790
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 16 days ago by 10k • written 6.2 years ago by ▴ 10
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression transcriptome
updated 21 days ago by 43k • written 9.0 years ago by • 0
3
votes
3
replies
348
views
genome assembly records not present in assembly_summary.txt
ncbi bacteria assembly
updated 13 days ago by 142k • written 13 days ago by ▴ 10
1
vote
3
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312
views
True variants selection
vcf bcftools
updated 27 days ago by ★ 1.9k • written 28 days ago by • 0
5
votes
3
replies
348
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 27 days ago by ★ 3.8k • written 28 days ago by ★ 5.3k
3
votes
3
replies
243
views
Genbank vs SRA
ncbi genbank genomics sra
updated 17 days ago by ★ 27k • written 17 days ago by ▴ 520
1
vote
3
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284
views
TaxID mapping file
annotation blobtools RNAseq decontamination transcriptomes
4 days ago by Lada ▴ 30
1
vote
3
replies
351
views
Why is DESeq2 normalization making my top feature have identical values across samples?
DESEQ2 WGCNA
28 days ago by DNAngel ▴ 250
2
votes
3
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983
views
Method to detect genome doubling
CNV genome doubling
updated 17 days ago by 4.2k • written 4.5 years ago by ▴ 750
3
votes
3
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535
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 19 days ago by 14k • written 20 days ago by ▴ 580
0
votes
3
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1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST E-value Blastp Protein
updated 22 days ago by 43k • written 5.3 years ago by • 0
0
votes
3
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171
views
bcftools - reducing to "sites-only"?
sites-only bcftools
updated 6 hours ago by 161k • written 20 hours ago by • 0
1
vote
3
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277
views
Bedtools merge minimum overlap?
bedtools genomics
updated 6 days ago by 35k • written 6 days ago by • 0
0
votes
3
replies
298
views
KEGG Pathways
r RNA-seq
updated 9 days ago by 43k • written 9 days ago by • 0
0
votes
3
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445
views
JASPAR2024_getMatrixSet error
JASPAR2024 getMatrixSet
updated 4 hours ago by 43k • written 11 weeks ago by ▴ 10
0
votes
3
replies
540
views
python file for coding potential calculator
cpc2.py
updated 16 days ago by ▴ 30 • written 21 days ago by • 0
1
vote
3
replies
6.2k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID org.Dr.eg.db
updated 22 days ago by 43k • written 5.6 years ago by ▴ 170
1
vote
3
replies
240
views
Problem with Seurat package in PercentageFeatureSet function
cell single
updated 18 minutes ago by ★ 2.4k • written 4 days ago by ▴ 60
1
vote
3
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3.4k
views
How to correct for batch effect in microarray meta-analysis
ComBat microarray meta-analysis batch-effect
updated 21 days ago by 43k • written 10.0 years ago by ▴ 120
2
votes
3
replies
990
views
Treating "patient" as a batch effect
ComBat_seq DESeq2 batch-Effect
updated 22 days ago by 43k • written 17 months ago by ▴ 20
0
votes
3
replies
299
views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
updated 15 days ago by 100k • written 16 days ago by • 0
0
votes
3
replies
674
views
Pluritest for pluripotency broken
pluripotent pluritest cells stem
updated 10 hours ago by • 0 • written 21 months ago by • 0
3
votes
3
replies
347
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 13 days ago by 14k • written 14 days ago by • 0
1
vote
3
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440
views
Extracting data from a local NCBI taxonomy database
R NCBI xml E-utilities Blast
updated 25 days ago by ▴ 60 • written 5 weeks ago by ▴ 150
1
vote
3
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4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 21 days ago by 43k • written 7.7 years ago by ★ 1.2k
0
votes
3
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435
views
why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
9 days ago by Assa Yeroslaviz ★ 1.8k
3
votes
3
replies
455
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
22 days ago by ayushm64 • 0
3
votes
3
replies
264
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide Genomic Sequence Uniprot Proteins
updated 17 days ago by 142k • written 17 days ago by ▴ 40
2
votes
3
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1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq edgeR batch-effect
updated 21 days ago by 43k • written 3.6 years ago by ▴ 20
10
votes
3
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273
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 1 day ago by ▴ 180 • written 2 days ago by • 0
1
vote
3
replies
297
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA illumina GEO metadata
updated 8 days ago by 142k • written 9 days ago by • 0
1
vote
3
replies
397
views
Ensembl gene id conversion
biomart ensembl
updated 23 days ago by 82k • written 25 days ago by • 0
1
vote
3
replies
120
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 8 hours ago by 161k • written 9 hours ago by ▴ 10
1
vote
3
replies
388
views
cellranger error message
multiplexing cellranger
updated 1 hour ago by • 0 • written 12 weeks ago by ▴ 10
931 results • Page 7 of 19
Recent Votes
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
cellranger error message
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Network plot from expression data in R using igraph
Comment: RNA seq analysis
RNA seq analysis
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Recent Replies
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length by marco.barr ▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length by marco.barr ▴ 100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message by Max • 0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s…
Comment: Different output for read length by marco.barr ▴ 100
Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length by GenoMax 142k
Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis by s.ghazala • 0
Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 100
Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS by tim.booth ▴ 50
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile by tim.booth ▴ 50
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length by Pierre Lindenbaum 161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file by sainavyav22 • 0
Here you go. 1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput 2.perl annotate_variation.pl 100…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant. Your question is ambiguous because you…
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