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1,000 results • Page 5 of 20
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5
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5
replies
2.1k
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batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 11 days ago by 43k • written 5.3 years ago by • 0
3
votes
5
replies
480
views
Having trouble building VG in Ubuntu
vg
updated 15 days ago by 43k • written 17 days ago by • 0
0
votes
5
replies
1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA lncRNA
updated 23 days ago by 43k • written 2.6 years ago by • 0
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
0
votes
5
replies
1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 19 days ago by 43k • written 6.4 years ago by ▴ 90
2
votes
5
replies
461
views
Marking duplicates using UMIs
Deduplication UMI
updated 7 days ago by 19k • written 8 days ago by • 0
0
votes
5
replies
333
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 1 day ago by 100k • written 5 days ago by ▴ 10
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 18 days ago by • 0 • written 3.8 years ago by ★ 1.8k
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 11 days ago by 43k • written 5.1 years ago by ★ 1.9k
1
vote
5
replies
716
views
RNA seq differential expression analysis
RNA-seq normalization
updated 9 days ago by ★ 1.7k • written 11 days ago by • 0
0
votes
5
replies
548
views
seg fault, core dumped with manta 1.6.0
manta gdb
updated 20 days ago by 43k • written 24 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
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer MSA intron-exon
updated 23 days ago by • 0 • written 6.6 years ago by ▴ 630
0
votes
5
replies
335
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 3 days ago by 141k • written 4 days ago by ▴ 90
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 14 days ago by ▴ 200 • written 16 months ago by ★ 1.4k
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 12 days ago by 43k • written 21 months ago by ▴ 60
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 9 days ago by • 0 • written 6.5 years ago by ▴ 30
3
votes
5
replies
558
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
7 days ago by n_navy • 0
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA gene-expression DESeq2 RNA-seq batch-effect
updated 12 days ago by 43k • written 12 months ago by ▴ 110
0
votes
5
replies
603
views
How to deeply sequence long inserts
Long-read phage NGS
updated 23 days ago by 43k • written 5 months ago by • 0
0
votes
5
replies
322
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
5 days ago by njornet ▴ 20
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq countOverlaps R
updated 12 days ago by 43k • written 6.3 years ago by ★ 1.9k
3
votes
5
replies
1.3k
views
NextGen Sequencing Folks, what do you keep as your raw backup? BCL's or FASTQ's? Both?
next-gen-sequencing backups data-storage
updated 23 days ago by 43k • written 2.1 years ago by ▴ 130
2
votes
5
replies
365
views
WGCNA website
wgcna
updated 22 days ago by 141k • written 24 days ago by ★ 1.7k
2
votes
5
replies
540
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 8 days ago by ★ 27k • written 9 days ago by • 0
3
votes
5
replies
281
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 7 days ago by 141k • written 7 days ago by • 0
1
vote
5
replies
574
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 9 days ago by 141k • written 9 days ago by • 0
2
votes
5
replies
2.3k
views
DGE on transcriptomic data, focus on transcript sequences or in derivated ORFs?
differential-gene-expression RNA-Seq ORFs
updated 19 days ago by 43k • written 6.4 years ago by ▴ 90
2
votes
5
replies
703
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
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R RNA-Seq limma DE batch-effect
updated 11 days ago by 43k • written 4.8 years ago by ▴ 60
8
votes
5
replies
5.4k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq batch-effect
updated 12 days ago by 43k • written 4.7 years ago by • 0
1
vote
5
replies
383
views
Best way to deal with overlapping read names in merged BAM files
picard MarkDuplicates
13 days ago by shpak.max ▴ 50
0
votes
5
replies
502
views
Is it possible to set different tracks to the same scale in JBrowse
track jbrowse
updated 16 days ago by 43k • written 18 days ago by • 0
0
votes
5
replies
296
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 24 days ago by 43k • written 28 days ago by ▴ 150
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 20 days ago by 3.2k • written 3.4 years ago by • 0
4
votes
5
replies
362
views
merging tetraploid vcf files through bcftools
vcf bcftools
27 days ago by analyst ▴ 30
2
votes
5
replies
489
views
Creating an index from multiple .fsa files
HISAT2 BWA Alignment
20 days ago by theworldsagainstme • 0
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 19 days ago by 43k • written 4.6 years ago by ▴ 20
1
vote
5
replies
2.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 17 days ago by 82k • written 5.1 years ago by ▴ 750
5
votes
5
replies
860
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 16 days ago by 43k • written 10 months ago by ▴ 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
674
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 23 days ago by 43k • written 6 weeks ago by • 0
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression RNA-Seq
updated 19 days ago by 43k • written 5.5 years ago by ▴ 100
0
votes
5
replies
876
views
extraction of spanning long reads
long-reads
updated 23 days ago by 43k • written 17 months ago by ▴ 110
1
vote
5
replies
603
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 5 days ago by • 0 • written 3 months ago by • 0
0
votes
5
replies
339
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate BUSCO.
updated 24 days ago by 141k • written 24 days ago by ▴ 10
1
vote
5
replies
1.5k
views
Blastn in galaxy
Blastn galaxy
updated 26 days ago by 43k • written 3.0 years ago by • 0
2
votes
5
replies
307
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
5 hours ago by analyst ▴ 30
2
votes
5
replies
392
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
17 hours ago by ashaneev07 ▴ 20
1,000 results • Page 5 of 20
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
A: Insert Size And Fragment Size ?
A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
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
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Recent Replies
Comment: Can I merge Hi-C fastq files from different lanes? by GenoMax 141k
If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
Comment: What should I consider as FASTA for dataset? by GenoMax 141k
> Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? What analysis are you trying to use the data fo…
Comment: Is it possible to bulk download files from GEO repository? by GenoMax 141k
Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
Answer: Two references 1. genome 2. plasmid for bowtie2 by GenoMax 141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
Answer: High Malat-1 expression in single cell data by ATpoint 82k
My comment is general since I've never looked at this gene specifically, but metrics of poor cell quality in my experience never come alone…
Comment: What does it mean single base resolution in sequencing? by GenoMax 141k
>You known, 90% + genomic region is transcripted. So, total RNA-seq theoretically covers most genome region. Perhaps but not all of that …
Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous by trausch ★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated by i.sudbery 19k
Thats very intersting! What are the features in your classifier?
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by hagl ▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes by Mohamed Abderrahmane ▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better? by Lluís R. ★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
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
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