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794 results • Page 2 of 16
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9
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597
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Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 1 day ago by ★ 2.0k • written 10 days ago by ▴ 140
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
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
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 13 days ago by • 0 • written 2.2 years ago by • 0
1
vote
9
replies
1.3k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 29 days ago by • 0 • written 20 months ago by ▴ 10
1
vote
9
replies
393
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 7 days ago by 19k • written 10 days ago by ★ 1.8k
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
0
votes
8
replies
529
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
0
votes
8
replies
459
views
Error in cnetplot enrichplot package
R
updated 24 days ago by 43k • written 24 days ago by • 0
1
vote
8
replies
127
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
34 minutes ago by ashkan ▴ 160
2
votes
8
replies
378
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
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
0
votes
8
replies
452
views
Different output for read length
samtools BAM
7 days ago by marco.barr ▴ 130
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
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
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
8
votes
8
replies
750
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 22 days ago by 14k • written 23 days ago by ▴ 10
3
votes
8
replies
681
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
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
1
vote
8
replies
542
views
Downsampling fastq file
downsample fastq
16 days ago by marco.barr ▴ 130
3
votes
8
replies
597
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
945
views
Adding CB tag to bam file
samtools bam
updated 22 days ago by 161k • written 28 days ago by • 0
1
vote
7
replies
608
views
ScRNA data question
scRNA Vlnplot Samples
updated 17 days ago by ★ 2.5k • written 22 days ago by ▴ 10
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
0
votes
7
replies
429
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
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
4
votes
7
replies
409
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
3
votes
7
replies
410
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
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
1
vote
7
replies
611
views
gvcf joint calling
WES GATK VCF gVCF
19 days ago by zihanss • 0
4
votes
7
replies
357
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 1 hour ago by ▴ 130 • written 1 day ago by ▴ 20
1
vote
7
replies
496
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
14 days ago by eebloom ▴ 80
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
0
votes
7
replies
636
views
Post-imputation plot
michigan-imputation-server quality-control
updated 14 days ago by 3.9k • written 17 days ago by ▴ 10
2
votes
7
replies
943
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
17 days ago by e.r.zakiev ▴ 210
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
5
votes
7
replies
485
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
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 4.1 years ago by ▴ 500
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
6
votes
7
replies
386
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
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
1
vote
7
replies
383
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
2 days ago by ntsopoul ▴ 60
1
vote
7
replies
536
views
Question regarding WGCNA
WGCNA Network-construction
7 days ago by deepak • 0
7
votes
6
replies
590
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
25 days ago by analyst ▴ 50
0
votes
6
replies
420
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 3 days ago by 43k • written 6 days ago by • 0
4
votes
6
replies
802
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 20 days ago by ★ 6.0k • written 24 days ago by ▴ 10
2
votes
6
replies
5.3k
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 28 days ago by 43k • written 3.8 years ago by • 0
3
votes
6
replies
752
views
Ciriquant not configuring hisat2 indexed files
ciriquant
25 days ago by Atul K. • 0
0
votes
6
replies
474
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 13 days ago by 14k • written 14 days ago by • 0
794 results • Page 2 of 16
Recent Votes
Answer: Details on salmon index
Comment: zero TPM for many gene including housekeeping when using kallisto
Sequence Alignment from Scratch with BWA
Answer: mitochondrial genome assembly pipeline
Comment: Help! Reconstruction of locus, order contigs
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
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Recent Replies
Comment: Help! Reconstruction of locus, order contigs by GenoMax 142k
Please use `ADD REPLY/ADD COMMENT` when responding to existing content. `SUBMIT ANSWER` is for new answers to the original question.
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…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
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