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794 results • Page 5 of 16
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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
2
votes
1
reply
332
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 13 days ago by 10k • written 17 days ago by ▴ 10
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
2
votes
2
replies
349
views
Association study using SNP data
Association Allele Parentage SNP
11 days ago by drajangirija • 0
2
votes
2
replies
312
views
p-value in CIBERSORT
CIBERSORT p-value
16 days ago by michelafrancesconi9 ▴ 20
2
votes
4
replies
329
views
from row count to tpm
tpm row-count normalization
updated 16 days ago by 43k • written 24 days ago by ▴ 20
2
votes
3
replies
209
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 2 days ago by 43k • written 2 days ago by • 0
2
votes
5
replies
641
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 26 days ago by ★ 27k • written 27 days ago by • 0
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 28 days ago by 43k • written 4.8 years ago by ▴ 20
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 29 days ago by 43k • written 4.8 years ago by ▴ 60
2
votes
3
replies
335
views
Problem with Seurat package in PercentageFeatureSet function
cell single
updated 7 days ago by ★ 2.5k • written 12 days ago by ▴ 60
2
votes
1
reply
233
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 6 days ago by 161k • written 6 days ago by ▴ 70
2
votes
3
replies
382
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 24 days ago by ★ 27k • written 25 days ago by ▴ 120
2
votes
3
replies
846
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 12 days ago by • 0 • written 7 months ago by • 0
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 28 days ago by 43k • written 7.3 years ago by ▴ 20
2
votes
4
replies
273
views
Where to get the following bed file?
WES bed reference file
updated 10 days ago by 142k • written 10 days ago by • 0
2
votes
3
replies
273
views
Finding variants within a subset of a BAM file
variant calling
2 days ago by ramiro.barrantes • 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 1 day ago by 43k • written 3.9 years 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
2
votes
5
replies
423
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
21 days ago by Lada ▴ 30
2
votes
11
replies
628
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
5 hours ago by egascon • 0
2
votes
5
replies
406
views
Importing a fastq file
Fastq
updated 7 days ago by ▴ 120 • written 8 days ago by • 0
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat RNA-Seq batch-effect sva
updated 29 days ago by 43k • written 4.8 years ago by • 0
2
votes
3
replies
501
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
29 days ago by valentinatsar • 0
2
votes
3
replies
401
views
Editing Human Reference Genome by adding a CDS
gff agat transcriptome
updated 29 days ago by 54k • written 29 days ago by ▴ 340
2
votes
2
replies
243
views
Raw counts using stringtie
stringtie RNA-seq
updated 13 days ago by 142k • written 13 days ago by • 0
2
votes
4
replies
219
views
Help with IGV abbreviation
igv
updated 2 days ago by 43k • written 3 days ago by • 0
2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 2 days ago by 43k • written 8 days ago by • 0
2
votes
6
replies
380
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
2
votes
3
replies
278
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
4 days ago by Azra ▴ 10
2
votes
3
replies
206
views
ggrepel function: geom_text_repel()
ggplot2 ggrepel R
updated 14 hours ago by 43k • written 1 day ago by ▴ 20
2
votes
2
replies
393
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment gaps
updated 19 days ago by ▴ 770 • written 22 days ago by • 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq alignment RNA-Seq featureCounts STAR
updated 3 days ago by ▴ 340 • written 4.9 years ago by ▴ 70
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq edgeR batch-effect
updated 28 days ago by 43k • written 3.6 years ago by ▴ 20
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq batch-effect
updated 28 days ago by 43k • written 5.1 years ago by ▴ 60
2
votes
5
replies
535
views
Marking duplicates using UMIs
Deduplication UMI
updated 25 days ago by 19k • written 26 days ago by • 0
2
votes
2
replies
219
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 17 days ago by 82k • written 17 days ago by • 0
2
votes
4
replies
262
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell seurat 10XGenomics scRNAseq
updated 1 day ago by ▴ 90 • written 1 day ago by ▴ 20
2
votes
5
replies
538
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
18 days ago by ashaneev07 ▴ 20
2
votes
2
replies
428
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
28 days ago by nhaus ▴ 360
2
votes
8
replies
378
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 4 days ago by 161k • written 5 days ago by ▴ 100
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
2
replies
195
views
genome finishing
finishing genome
updated 1 day ago by ▴ 20 • written 2 days ago by • 0
2
votes
3
replies
995
views
Method to detect genome doubling
CNV genome doubling
updated 25 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
3
replies
390
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 21 days ago by ★ 6.0k • written 5 weeks ago by ▴ 60
2
votes
5
replies
567
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 4 days ago by ▴ 40 • written 13 days ago by ▴ 30
2
votes
5
replies
268
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 3 days ago by 8.5k • written 3 days ago by • 0
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 22 days ago by • 0 • written 2.5 years ago by • 0
2
votes
2
replies
181
views
Cannot install bwa-mem2 via conda
conda mamba python
updated 22 hours ago by 43k • written 1 day ago by • 0
2
votes
2
replies
197
views
Genome Visualization Tools
bacterial genome
updated 2 days ago by 142k • written 2 days ago by ▴ 10
794 results • Page 5 of 16
Recent Votes
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
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
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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…
Answer: Help! Reconstruction of locus, order contigs by BATMAN • 0
Is there any way to get the ordering of each genome in .gbk format from progressiveMauve?
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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