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1,000 results • Page 6 of 20
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3
votes
1
reply
169
views
NCBI CLI Download all proteins from Taxid
ncbi
updated 26 days ago by 141k • written 26 days ago by ★ 1.9k
2
votes
3
replies
319
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 6 days ago by ★ 27k • written 6 days ago by ▴ 120
2
votes
1
reply
864
views
Multiple BAM files (ccs) input with Lima (PacBio)
Long-read-sequencing PacBio
updated 23 days ago by 43k • written 2.8 years ago by ▴ 10
2
votes
4
replies
6.1k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect RNA-Seq R DESeq2
updated 10 days ago by 43k • written 7.6 years ago by ▴ 70
2
votes
6
replies
465
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
17 days ago by sansan_96 ▴ 80
2
votes
2
replies
395
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO velocity count-matrix
updated 12 days ago by 43k • written 13 days ago by • 0
2
votes
5
replies
674
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 23 days ago by 43k • written 6 weeks ago by • 0
2
votes
9
replies
850
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 5 days ago by 4.2k • written 6 months ago by • 0
2
votes
1
reply
621
views
Job: Exciting 2024 Summer Internship Opportunity in Translational Genetics Arrowhead Pharmaceuticals!
intern
23 days ago by Shicheng Guo ★ 9.4k
2
votes
2
replies
292
views
what is the purpose of indexing the reference genome (Kallisto)
indexing Kallisto
updated 2 days ago by ★ 5.9k • written 3 days ago by ▴ 10
2
votes
1
reply
294
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun metagenomics blastp taxonomy
updated 9 days ago by 141k • written 9 days ago by • 0
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq R seurat harmony batch-effect
updated 10 days ago by 43k • written 3.7 years ago by • 0
2
votes
3
replies
2.1k
views
Why the PCA results of PCASamples() from methylkit is different from prcomp()?
methylkit prcomp pca PCASamples multiplePCA
updated 22 days ago by ★ 1.2k • written 4.2 years ago by ▴ 250
2
votes
2
replies
212
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 1 hour ago by 19k • written 2 days ago by ▴ 40
2
votes
6
replies
609
views
Hybrid assembly Pacbio- Nanopore
long-reads hybric assembly genome short-reads
24 days ago by Lissa Cruz Saavedra • 0
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch limma removeBatchEffect rna-seq batch-effect
updated 12 days ago by 43k • written 21 months ago by ▴ 20
2
votes
3
replies
931
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 13 days ago by 43k • written 4.1 years ago by ▴ 790
2
votes
4
replies
1.2k
views
PLINK p value returning NA
GWAS PLINK
updated 20 days ago by 10k • written 18 months ago by • 0
2
votes
5
replies
299
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
3 hours ago by analyst ▴ 30
2
votes
5
replies
2.2k
views
Generating a heatmap in DEG analysis
Differential-gene-expression RNA-Seq
updated 19 days ago by 43k • written 3.1 years ago by ▴ 10
2
votes
5
replies
460
views
Marking duplicates using UMIs
Deduplication UMI
updated 7 days ago by 19k • written 8 days ago by • 0
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 7 days ago by 43k • written 10.6 years ago by ▴ 150
2
votes
2
replies
299
views
Creating a cytoscape bubble figure
cytoscape network GO
17 days ago by Dave Carlson ★ 1.7k
2
votes
5
replies
312
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
3 days ago by Lada ▴ 30
2
votes
4
replies
323
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
5 days ago by HyperEvo • 0
2
votes
1
reply
169
views
multiple reference sequences
freebayes
updated 26 days ago by 141k • written 26 days ago by ▴ 10
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 10 days ago by 43k • written 18 months ago by • 0
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta Nanopore long-read fastq
updated 23 days ago by 43k • written 2.9 years ago by ▴ 10
2
votes
4
replies
374
views
How to I use prefetch (SRAtoolkit) on multiple accessions all at one?
sratoolkit prefetch
updated 22 days ago by 161k • written 22 days ago by ▴ 100
2
votes
5
replies
700
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 8 days ago by ▴ 740 • written 9 days ago by ★ 2.4k
2
votes
3
replies
303
views
Using GPUs in snakemake
Parabricks gpu snakemake slurm
19 days ago by raphael.B ▴ 520
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads RNA-seq gene-expression read-count
updated 23 days ago by 43k • written 2.9 years ago by • 0
2
votes
1
reply
304
views
How to highlight genes on genome visual reprezentation/what tool to use?
gene genome
updated 15 days ago by 35k • written 15 days ago by ▴ 10
2
votes
4
replies
326
views
SnpEff annotates coding duplication as intronic?
snpeff
12 days ago by kirill.zaslavsky • 0
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq ComBat-seq SVA edgeR batch-effect
updated 12 days ago by 43k • written 3.5 years ago by ▴ 50
2
votes
2
replies
2.1k
views
How to use pacbio reads to join contigs
assembly tgs pacbio
updated 23 days ago by 43k • written 6.0 years ago by ▴ 20
2
votes
5
replies
365
views
WGCNA website
wgcna
updated 22 days ago by 141k • written 24 days ago by ★ 1.7k
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 9 hours ago by ★ 7.0k • written 8 months ago by ▴ 10
2
votes
2
replies
585
views
Does the Minion demultiplex when basecalling?
minion minknow long-read
updated 23 days ago by 43k • written 21 months ago by • 0
2
votes
4
replies
307
views
I am unsure why my files are not being accepted in bedtools jaccard, any tips?
bedtools
26 days ago by Ronin • 0
2
votes
1
reply
958
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression RNA-Seq R DESeq2
updated 19 days ago by 43k • written 4.0 years ago by ▴ 310
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell RNA-Seq batch-effect
updated 11 days ago by 43k • written 5.9 years ago by ▴ 60
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression R limma batch-effect model-matrix
updated 10 days ago by 43k • written 7.2 years ago by ▴ 20
2
votes
6
replies
868
views
Batch effect correction with cell type enrichment analysis
limma RNA-seq r batch-effect
updated 12 days ago by 43k • written 19 months ago by ▴ 140
2
votes
5
replies
1.0k
views
Ties in reranked list
fgsea GSEA
updated 15 days ago by • 0 • written 7 months ago by • 0
2
votes
3
replies
957
views
Method to detect genome doubling
CNV genome doubling
updated 6 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
27 days ago by b.contreras.moreira ▴ 170
2
votes
7
replies
519
views
STARsolo ; Reads are NOT mapped to transcriptome
STARsolo
updated 17 days ago by 141k • written 19 days ago by • 0
2
votes
3
replies
984
views
Treating "patient" as a batch effect
ComBat_seq DESeq2 batch-Effect
updated 12 days ago by 43k • written 17 months ago by ▴ 20
2
votes
5
replies
489
views
Creating an index from multiple .fsa files
HISAT2 BWA Alignment
20 days ago by theworldsagainstme • 0
1,000 results • Page 6 of 20
Recent Votes
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: Longitudinal analysis of subpopulations: which approach is better? by ATpoint 82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file by marco.barr ▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers by christopher medway ▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
Comment: ChIP-seq datasets: input samples omitted? by i.sudbery 19k
Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)? by i.sudbery 19k
See the section on non full rank design matrices in the DESeq2 manual. In this case your problem is that healthy and 0dpi samples are e…
Comment: NGS forensics: how to know if data is fabricated by i.sudbery 19k
Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated by i.sudbery 19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing? by jinyu ▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
Answer: Is it possible to bulk download files from GEO repository? by atharvakarkare14 ▴ 10
Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing? by Ruqaiya • 0
OK. Problem solved. The problem was from my end. Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated by Mensur Dlakic ★ 27k
Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated by Prash ▴ 280
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
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