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762 results • Page 2 of 16
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2
votes
9
replies
938
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 23 days ago by 4.2k • written 7 months ago by • 0
4
votes
9
replies
378
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
4 hours ago by Gabriel R. ★ 2.9k
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 18 days ago by 43k • written 8 months ago by • 0
0
votes
8
replies
530
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
4
votes
8
replies
765
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
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 27 days ago by 14k • written 9 months ago by ▴ 80
0
votes
8
replies
461
views
Error in cnetplot enrichplot package
R
updated 24 days ago by 43k • written 24 days ago by • 0
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
8
votes
8
replies
751
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 22 days ago by 14k • written 23 days ago by ▴ 10
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray batch-effect
updated 29 days ago by 43k • written 9.7 years ago by • 0
1
vote
8
replies
949
views
Adding CB tag to bam file
samtools bam
updated 22 days ago by 161k • written 28 days ago by • 0
0
votes
8
replies
452
views
Different output for read length
samtools BAM
7 days ago by marco.barr ▴ 130
1
vote
8
replies
544
views
Downsampling fastq file
downsample fastq
17 days ago by marco.barr ▴ 130
2
votes
8
replies
379
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 5 days ago by 161k • written 5 days ago by ▴ 100
3
votes
8
replies
600
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
10 days ago by Qroid ▴ 40
3
votes
8
replies
682
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 15 days ago by ▴ 100
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 29 days ago by 43k • written 4.6 years ago by ▴ 180
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 29 days ago by 43k • written 5.0 years ago by ▴ 140
2
votes
7
replies
947
views
Removing duplicates
duplicates ONT minimap2
updated 28 days ago by ▴ 580 • written 4 weeks ago by • 0
4
votes
7
replies
633
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
18 days ago by e.r.zakiev ▴ 210
3
votes
7
replies
410
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
18 days ago by salias • 0
6
votes
7
replies
387
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
0
votes
7
replies
432
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 4 days ago by ▴ 20 • written 18 days ago by • 0
4
votes
7
replies
411
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 22 days ago by ▴ 860 • written 6.2 years ago by ▴ 10
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 28 days ago by 82k • written 7.2 years ago by ▴ 80
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
1
vote
7
replies
610
views
ScRNA data question
scRNA Vlnplot Samples
updated 18 days ago by ★ 2.5k • written 22 days ago by ▴ 10
1
vote
7
replies
498
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
14 days ago by eebloom ▴ 80
4
votes
7
replies
421
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 5 hours ago by ▴ 130 • written 2 days ago by ▴ 20
4
votes
7
replies
605
views
To get p-values for the TPM
P-value TPM RSEM
updated 22 days ago by ★ 6.0k • written 23 days ago by • 0
0
votes
7
replies
638
views
Post-imputation plot
michigan-imputation-server quality-control
updated 14 days ago by 3.9k • written 18 days ago by ▴ 10
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 29 days ago by 43k • written 4.1 years ago by ▴ 500
1
vote
7
replies
386
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
2 days ago by ntsopoul ▴ 60
1
vote
7
replies
612
views
gvcf joint calling
WES GATK VCF gVCF
19 days ago by zihanss • 0
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by • 0 • written 5.7 years ago by ▴ 20
5
votes
7
replies
487
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
1
vote
7
replies
538
views
Question regarding WGCNA
WGCNA Network-construction
8 days ago by deepak • 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 29 days ago by 6.4k • written 10.9 years ago by ▴ 10
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 17 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
0
votes
6
replies
475
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 13 days ago by 14k • written 14 days ago by • 0
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 21 days ago by 82k • written 3.9 years ago by ▴ 280
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 11 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
7
votes
6
replies
590
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
26 days ago by analyst ▴ 50
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 21 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
4
votes
6
replies
806
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 20 days ago by ★ 6.0k • written 24 days ago by ▴ 10
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma gwas
updated 18 days ago by • 0 • written 5.0 years ago by ▴ 90
1
vote
6
replies
727
views
anRichment is missing
WGCNA anRichment
updated 11 days ago by 142k • written 6 months ago by ▴ 180
3
votes
6
replies
754
views
Ciriquant not configuring hisat2 indexed files
ciriquant
25 days ago by Atul K. • 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 12 days ago by ▴ 10 • written 2.0 years ago by • 0
762 results • Page 2 of 16
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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Recent Replies
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs by BATMAN • 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
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