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827 results • Page 2 of 17
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0
votes
9
replies
341
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
22 hours ago by njornet ▴ 20
1
vote
9
replies
1.3k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 28 days ago by • 0 • written 20 months ago by ▴ 10
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
17 days ago by anna ▴ 20
3
votes
9
replies
940
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 28 days ago by ★ 2.4k • written 28 days ago by • 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 17 days ago by 43k • written 8 months ago by • 0
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 23 days ago by 4.2k • written 7 months ago by • 0
0
votes
9
replies
595
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
1 day ago by Arton ▴ 10
2
votes
9
replies
691
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 1 day ago by 161k • written 9 days ago by • 0
4
votes
8
replies
763
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 20 days ago by 35k • written 21 days ago by ▴ 10
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray batch-effect
updated 28 days ago by 43k • written 9.7 years ago by • 0
8
votes
8
replies
750
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 21 days ago by 14k • written 23 days ago by ▴ 10
3
votes
8
replies
575
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
10 days ago by Qroid ▴ 40
1
vote
8
replies
539
views
Downsampling fastq file
downsample fastq
16 days ago by marco.barr ▴ 120
0
votes
8
replies
449
views
Different output for read length
samtools BAM
7 days ago by marco.barr ▴ 120
0
votes
8
replies
458
views
Error in cnetplot enrichplot package
R
updated 24 days ago by 43k • written 24 days ago by • 0
6
votes
8
replies
666
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 29 days ago by 14k • written 4 weeks ago by ▴ 40
3
votes
8
replies
678
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 10 days ago by ▴ 410 • written 14 days ago by ▴ 100
1
vote
8
replies
944
views
Adding CB tag to bam file
samtools bam
updated 21 days ago by 161k • written 28 days ago by • 0
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 26 days ago by 14k • written 9 months ago by ▴ 80
2
votes
8
replies
374
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 4 days ago by 161k • written 4 days ago by ▴ 100
0
votes
8
replies
527
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 16 days ago by 4.2k • written 18 days ago by ▴ 10
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 29 days ago by 43k • written 7.1 years ago by ▴ 20
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 14 days ago by • 0 • written 5.1 years ago by 11k
3
votes
8
replies
4.2k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm scRNA-seq RNA-Seq tpm batch-effect
updated 28 days ago by 43k • written 4.6 years ago by ▴ 180
4
votes
7
replies
397
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
1
vote
7
replies
485
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
13 days ago by eebloom ▴ 80
0
votes
7
replies
633
views
Post-imputation plot
michigan-imputation-server quality-control
updated 14 days ago by 3.9k • written 17 days ago by ▴ 10
0
votes
7
replies
421
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 3 days ago by ▴ 20 • written 17 days ago by • 0
4
votes
7
replies
604
views
To get p-values for the TPM
P-value TPM RSEM
updated 21 days ago by ★ 6.0k • written 22 days ago by • 0
4
votes
7
replies
631
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
17 days ago by e.r.zakiev ▴ 210
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 29 days ago by 43k • written 4.4 years ago by ▴ 360
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 18 days ago by ★ 7.2k • written 8 months ago by ▴ 10
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 29 days ago by 43k • written 7.7 years ago by ▴ 70
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 28 days ago by 43k • written 4.0 years ago by ▴ 500
1
vote
7
replies
608
views
gvcf joint calling
WES GATK VCF gVCF
18 days ago by zihanss • 0
1
vote
7
replies
377
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
2 days ago by ntsopoul ▴ 60
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 5 days ago by • 0 • written 5.7 years ago by ▴ 20
1
vote
7
replies
608
views
ScRNA data question
scRNA Vlnplot Samples
updated 17 days ago by ★ 2.4k • written 21 days ago by ▴ 10
6
votes
7
replies
382
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
1
vote
7
replies
536
views
Question regarding WGCNA
WGCNA Network-construction
7 days ago by deepak • 0
5
votes
7
replies
483
views
RNA seq analysis
DESeq RNA-seq
1 day ago by Jacek ▴ 20
2
votes
7
replies
940
views
Removing duplicates
duplicates ONT minimap2
updated 28 days ago by ▴ 580 • written 29 days ago by • 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 27 days ago by 82k • written 7.2 years ago by ▴ 80
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 28 days ago by 43k • written 5.0 years ago by ▴ 140
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 21 days ago by ▴ 860 • written 6.2 years ago by ▴ 10
3
votes
7
replies
404
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
17 days ago by salias • 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 20 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
4
votes
6
replies
4.0k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 29 days ago by 43k • written 4.8 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 8 days ago by ▴ 10 • written 2.5 years ago by • 0
827 results • Page 2 of 17
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Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Answer: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err by Nikki Harris • 0
Hello It appears that the file path or file permissions may be the cause of the problem. Verify that the file "/geneInfo.tab" is present…
Comment: Add line under stat test by Nyksubuz ▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite by dario.garvan ▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by GenoMax 142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo. by Ram 43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
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