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1,000 results • Page 3 of 20
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4
votes
6
replies
321
views
Protein loops
protein Loop
4 weeks ago by Curious ▴ 10
4
votes
6
replies
1.2k
views
Transcript quantification
rna-seq transcriptome SRA
updated 10 months ago by 81k • written 10 months ago by • 0
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 22 days ago by 43k • written 5.5 years ago by ▴ 110
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 9 days ago by 43k • written 3.7 years ago by ▴ 20
4
votes
6
replies
2.6k
views
Convert Nanopore Fast5 files to Fasta format
fast5 fasta Nanopore
11 months ago by Sowmya Pulapet ▴ 70
4
votes
7
replies
2.1k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 10 weeks ago by 43k • written 21 months ago by ▴ 10
4
votes
14
replies
2.6k
views
Is it possible to annotate single genes by snpeff
snp vcf
updated 9 months ago by 43k • written 6.7 years ago by ▴ 70
4
votes
11
replies
605
views
Remove X in row name with only number
GSVA
updated 10 weeks ago by 43k • written 10 weeks ago by ▴ 260
4
votes
13
replies
987
views
Mapping FASTQ files of scRNA-seq to reference genome
star EBI cellranger scRNA-seq SRA
updated 3 months ago by 43k • written 3 months ago by ▴ 20
4
votes
8
replies
1.8k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers Enhancers
updated 11 weeks ago by ★ 16k • written 3 months ago by • 0
4
votes
6
replies
1.0k
views
Python script to automatically read in, name output files & parse R1 & R2 fastq.gz files when given an input directory with raw data files
python fastq
9 months ago by eorr ▴ 30
4
votes
7
replies
1.4k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 141k • written 9 months ago by • 0
4
votes
4
replies
593
views
I cannot install anaconda on ubuntu 22.04
ubuntu anaconda Conda
updated 8 months ago by 43k • written 8 months ago by ▴ 10
4
votes
5
replies
1.1k
views
STAR mapping - regarding output files content
STAR RNA-seq mapping
updated 8 months ago by ▴ 900 • written 8 months ago by • 0
4
votes
6
replies
1.8k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 9 months ago by 141k • written 9 months ago by • 0
4
votes
9
replies
540
views
variant calling
variant-calling
updated 14 days ago by 43k • written 15 days ago by • 0
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 7 months ago by ★ 1.4k • written 8 months ago by • 0
4
votes
8
replies
585
views
GCP Snakemake
snakemake GCP
updated 11 weeks ago by 43k • written 12 weeks ago by ▴ 10
4
votes
11
replies
1.7k
views
PCA WITH PLINK
PLINK
updated 8 months ago by 87k • written 8 months ago by • 0
4
votes
5
replies
529
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 8 months ago by 141k • written 8 months ago by • 0
4
votes
5
replies
364
views
Filter out miRNA from ncRNA dataset
bowtie bowtie2 miRNA filtering ncRNA
updated 8 weeks ago by 81k • written 8 weeks ago by ▴ 10
4
votes
9
replies
1.1k
views
Snakemake issue with wrappers
Python Snakemake
5 months ago by Begonia_pavonina ▴ 150
4
votes
1
reply
616
views
How to interpret Clustree results?
scRNA clustering clustree
updated 8 months ago by 3.9k • written 8 months ago by ▴ 120
4
votes
3
replies
666
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 8 months ago by 11k • written 8 months ago by ▴ 10
4
votes
16
replies
922
views
hisat2 location does not exist
hisat2
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
4
votes
6
replies
859
views
Hisat2 index and alignment question
ubuntu rna-seq index hisat2
updated 6 months ago by 100k • written 6 months ago by • 0
4
votes
2
replies
597
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 6 months ago by ★ 1.5k • written 6 months ago by ▴ 100
4
votes
3
replies
734
views
BBduk log and stats appear to be inconsistent
bbduk bbmap
updated 11 months ago by 141k • written 11 months ago by ★ 1.7k
4
votes
7
replies
799
views
SNP IDs
SNP
5 months ago by kl ▴ 10
4
votes
7
replies
521
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 4 days ago by 43k • written 5 days ago by ▴ 20
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast remote databases Blastplus
updated 9 months ago by 141k • written 2.3 years ago by • 0
4
votes
3
replies
574
views
Identifying enhancers that regulate certain genes
enhancers
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 40
4
votes
3
replies
737
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
7 months ago by stefano.iantorno ▴ 70
4
votes
4
replies
832
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 10 months ago by 43k • written 10 months ago by • 0
4
votes
3
replies
291
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 10 weeks ago by 4.6k • written 10 weeks ago by ▴ 30
4
votes
5
replies
772
views
Does adding reads cause batch effects?
kallisto RNAseq
10 months ago by bioinfo ▴ 150
4
votes
6
replies
622
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
4 months ago by Tihana ▴ 10
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 10 months ago by 43k • written 4.6 years ago by ▴ 120
4
votes
12
replies
7.7k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 10 weeks ago by ▴ 10 • written 3.3 years ago by ▴ 60
4
votes
8
replies
3.4k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 9 months ago by 43k • written 9.5 years ago by • 0
4
votes
16
replies
1.7k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 7 weeks ago by 43k • written 6 months ago by • 0
4
votes
2
replies
546
views
Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
SoupX
5 months ago by malonzm1 ▴ 20
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV WGS
updated 9 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
3
replies
576
views
Over Representation analysis altered pathways in common between comparisons plot
R Visualization DGE ORA
updated 6 months ago by ★ 2.0k • written 6 months ago by ▴ 10
4
votes
9
replies
980
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex illumina sequencing
updated 4 months ago by 141k • written 4 months ago by ▴ 120
4
votes
4
replies
589
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by 141k • written 8 months ago by ★ 2.9k
4
votes
1
reply
552
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
ClusterProfiler RNA-seq GSEA
updated 9 months ago by ★ 1.6k • written 9 months ago by ▴ 100
4
votes
7
replies
956
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by 4.5k • written 6 months ago by ▴ 20
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 9 months ago by 43k • written 11.3 years ago by ▴ 50
4
votes
3
replies
301
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 8 weeks ago by ★ 1.8k • written 9 weeks ago by ▴ 10
1,000 results • Page 3 of 20
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High fold change values
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Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
Error with Formatdb of legacy blast?
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
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Recent Replies
Comment: How to reduce the variation of CIBERSORTx results? by feather-W • 0
Hi LChart, Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
Comment: How to reduce the variation of CIBERSORTx results? by LChart 3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error? by 22211020193 • 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results? by feather-W • 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates by joe ▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates by samuel.a.odonnell ▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis by geneontologyhelp ▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data? by etiennedanis ▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates by joe ▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together? by GenoMax 141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions by swbarnes2 14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates by quentinperriere • 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results? by LChart 3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
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