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10
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16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 2 days ago by 161k • written 5.7 years ago by ▴ 180
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 6 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 4 days ago by • 0 • written 6.1 years ago by ▴ 20
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 14 hours ago by ▴ 180 • written 3.0 years ago by ▴ 20
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 1 day ago by • 0 • written 5.5 years ago by 8.4k
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 3 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 1 day ago by ▴ 90 • written 6.4 years ago by ▴ 60
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 5 days ago by • 0 • written 10.2 years ago by ▴ 20
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 1 day ago by • 0 • written 5.1 years ago by ★ 1.8k
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 6 days ago by • 0 • written 2.2 years ago by • 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 17 hours ago by 142k • written 3.2 years ago by ▴ 10
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 4 days ago by ▴ 10 • written 24 months ago by • 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR statistical test parametric non-parametric
updated 6 days ago by ▴ 210 • written 3.8 years ago by ▴ 40
4
votes
3
replies
1.7k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 16 hours ago by 161k • written 18 hours ago by ★ 1.2k
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 6 days ago by ★ 7.1k • written 4 months ago by ▴ 10
1
vote
2
replies
1.5k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring SCTransform Seurat
updated 1 day ago by • 0 • written 2.3 years ago by ▴ 10
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 1 day ago by • 0 • written 5.7 years ago by ▴ 30
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 1 day ago by ▴ 10 • written 2.5 years ago by • 0
1
vote
2
replies
1.1k
views
News: The GDC Legacy Archive is retiring soon.
genomic-data-commons tcga gdc
4 days ago by Zhenyu Zhang ★ 1.2k
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
4 days ago by Ibrahim Tanyalcin ★ 1.2k
1
vote
10
replies
858
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 3 days ago by • 0 • written 4 months ago by ▴ 30
2
votes
3
replies
820
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 5 days ago by • 0 • written 7 months ago by • 0
13
votes
14
replies
805
views
High Malat-1 expression in single cell data
single-cell
updated 1 day ago by ▴ 40 • written 10 days ago by ▴ 40
2
votes
4
replies
712
views
Count all variants from vcf file
variants vcf Count
updated 2 days ago by 161k • written 20 months ago by • 0
1
vote
6
replies
685
views
anRichment is missing
WGCNA anRichment
updated 3 days ago by 142k • written 5 months ago by ▴ 180
0
votes
3
replies
677
views
Pluritest for pluripotency broken
pluripotent pluritest cells stem
updated 19 hours ago by • 0 • written 21 months ago by • 0
10
votes
14
replies
657
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 2 days ago by 142k • written 8 days ago by • 0
5
votes
5
replies
622
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 6 days ago by • 0 • written 15 days ago by ★ 3.9k
3
votes
8
replies
603
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 3 days ago by ▴ 410 • written 7 days ago by ▴ 100
0
votes
1
reply
537
views
Job: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search job
updated 4 days ago by 142k • written 4 days ago by • 0
3
votes
8
replies
524
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
3 days ago by Qroid ▴ 40
1
vote
7
replies
477
views
Question regarding WGCNA
WGCNA Network-construction
14 hours ago by deepak • 0
0
votes
3
replies
461
views
JASPAR2024_getMatrixSet error
JASPAR2024 getMatrixSet
updated 13 hours ago by 43k • written 11 weeks ago by ▴ 10
1
vote
7
replies
459
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
6 days ago by eebloom ▴ 80
0
votes
2
replies
457
views
HLA-HD tool for genomic imputation
genomics imputation bash
updated 2 days ago by • 0 • written 3 months ago by ▴ 10
0
votes
7
replies
452
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 1 day ago by ★ 2.0k • written 3 days ago by ▴ 140
0
votes
6
replies
429
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 6 days ago by 14k • written 6 days ago by • 0
1
vote
3
replies
426
views
cellranger error message
multiplexing cellranger
updated 9 hours ago by • 0 • written 12 weeks ago by ▴ 10
3
votes
4
replies
418
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 3 days ago by ★ 7.1k • written 6 days ago by ▴ 40
1
vote
2
replies
416
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
1 day ago by Zeng Hao ▴ 40
3
votes
3
replies
406
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 hours ago by ▴ 770 • written 20 days ago by ▴ 60
1
vote
5
replies
403
views
HCL database download
HCL
updated 2 days ago by 43k • written 6 days ago by ▴ 20
1
vote
1
reply
390
views
ComBat_Seq stuck adjusting the data
Batch-Effect RNAseq ComBat-Seq
updated 17 hours ago by • 0 • written 4 months ago by ▴ 10
0
votes
4
replies
382
views
Highest variable features in single cell data
single-cell
2 days ago by carolofharvest ▴ 40
1
vote
5
replies
378
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 3 days ago by 43k • written 4 days ago by • 0
0
votes
5
replies
372
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 6 days ago by ▴ 180 • written 7 days ago by • 0
0
votes
5
replies
364
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 11 hours ago by 22k • written 2 days ago by • 0
1
vote
4
replies
362
views
Segmentation error while using a tool
smalt
updated 5 days ago by ★ 27k • written 6 days ago by • 0
1
vote
6
replies
361
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 6 days ago by 142k • written 24 days ago by ▴ 80
195 results • Page 1 of 4
Recent Votes
How to set a threshold for coefficient of variation in RNA-seq?
What is Deepvariant default filtering values ?
Answer: EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
How to plot the heatmap of gene expression for very large data set ?
Help with VG Toolkit: VCF Output is Empty
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Recent Replies
Comment: EdgeR - relationship between logFC and coefficients by gBioStar5 • 0
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients by Gordon Smyth ★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally by DGELRT are on the loge scale. If you convert from t…
Answer: Importing a fastq file by size_t ▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors by Philipp Bayer 8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
Comment: absolute path for symbolic links in Snakefile by Jesse ▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API by GenoMax 142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length by marco.barr ▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
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…
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