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1,000 results • Page 3 of 20
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4
votes
6
replies
622
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
5 months ago by Tihana ▴ 10
4
votes
3
replies
295
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
3
replies
578
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
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 25 days ago by 43k • written 5.5 years ago by ▴ 110
4
votes
6
replies
323
views
Protein loops
protein Loop
5 weeks ago by Curious ▴ 10
4
votes
7
replies
2.6k
views
low bootstrap value?
phylogeny genome alignment
updated 10 months ago by 43k • written 4.8 years ago by ▴ 120
4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog PCA vsd
updated 11 months ago by 81k • written 11 months ago by ▴ 160
4
votes
4
replies
837
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
5
replies
1.0k
views
VEP run with --af_gnomadg refuses to provide allele frequencies for extremely rare variants
vep gnomad
updated 8 months ago by ▴ 60 • written 8 months ago by 22k
4
votes
6
replies
2.4k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 10 months ago by • 0 • written 20 months ago by ▴ 20
4
votes
9
replies
1.1k
views
Snakemake issue with wrappers
Python Snakemake
5 months ago by Begonia_pavonina ▴ 150
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 12 days ago by 43k • written 3.7 years ago by ▴ 20
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
2
replies
547
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
7
replies
760
views
Alternative for grep in a for loop
linux
updated 6 months ago by 43k • written 6 months ago by ▴ 20
4
votes
14
replies
1.1k
views
remove white space in fastq file
fastq
updated 4 months ago by 141k • written 4 months ago by • 0
4
votes
6
replies
866
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
1
reply
554
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
527
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 6 days ago by 43k • written 7 days ago by ▴ 20
4
votes
2
replies
604
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
8
replies
3.5k
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
3
replies
673
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
11
replies
609
views
Remove X in row name with only number
GSVA
updated 10 weeks ago by 43k • written 10 weeks ago by ▴ 260
4
votes
3
replies
473
views
Parsing columns with awk
awk
updated 5 months ago by 43k • written 5 months ago by ▴ 300
4
votes
9
replies
556
views
variant calling
variant-calling
updated 17 days ago by 43k • written 18 days ago by • 0
4
votes
13
replies
994
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
7
replies
801
views
SNP IDs
SNP
5 months ago by kl ▴ 10
4
votes
16
replies
930
views
hisat2 location does not exist
hisat2
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
4
votes
4
replies
630
views
Feedback on mouse brain scRNA-seq quality control
mouse brain singe-cell scRNAseq quality-control
7 months ago by nshenoy ▴ 50
4
votes
11
replies
1.6k
views
Check Strandedness
Check_Strandedness how_are_we_stranded_here leafcutter bash
updated 6 months ago by 20k • written 8 months ago by • 0
4
votes
5
replies
773
views
Does adding reads cause batch effects?
kallisto RNAseq
10 months ago by bioinfo ▴ 150
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
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by 43k • written 6.8 years ago by ▴ 750
4
votes
9
replies
987
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
3
replies
384
views
Single cell analysis of Cancer
cancer single-cell RNA-seq
updated 9 weeks ago by 141k • written 9 weeks ago by ▴ 20
4
votes
2
replies
464
views
KEGG DATABASE
DATABASE KEGG
updated 4 months ago by ★ 1.8k • written 4 months ago by • 0
4
votes
3
replies
738
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
2.2k
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
8
replies
593
views
GCP Snakemake
snakemake GCP
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 10
4
votes
4
replies
782
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 10 months ago by 21k • written 11 months ago by ▴ 20
4
votes
3
replies
303
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 9 weeks ago by ★ 1.8k • written 9 weeks ago by ▴ 10
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
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
3
replies
575
views
Identifying enhancers that regulate certain genes
enhancers
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 40
4
votes
3
replies
743
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
7 months ago by stefano.iantorno ▴ 70
4
votes
6
replies
927
views
How to pass from DNA to AA fasta
genetics
updated 11 months ago by ★ 2.4k • written 11 months ago by • 0
4
votes
7
replies
966
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by 4.5k • written 6 months ago by ▴ 20
4
votes
5
replies
530
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
13
replies
794
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 3 days ago by ★ 1.7k • written 9 days 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 8 weeks ago by 43k • written 6 months ago by • 0
1,000 results • Page 3 of 20
Recent Votes
Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
Answer: Ubuntu storage space is decreasing automatically
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
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Recent Replies
Comment: MEGA Analysis Issue on High-Performance Computer by 5heikki 11k
16GB of RAM is nothing. My phone has that. My server has 1TB of RAM, and even that isn't always enough
Comment: MEGA Analysis Issue on High-Performance Computer by GenoMax 141k
I don't think MEGA supports GPU's: https://www.megasoftware.net/web_help_11/Part_I_Getting_Started/Installing_MEGA/System_Requirements.htm
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by ATpoint 81k
You can, if you use RStudio via Docker, for example `bioconductor/bioconductor_docker`. I currently manage many different projects with thi…
Comment: bam merging for archaic samples by Matteo Ungaro ▴ 100
@Pierre Lindenbaum I see. So, I can actually manipulate just one single RG tag at the time with `samtools`? Which flag should I use, or sho…
Comment: bam merging for archaic samples by Pierre Lindenbaum 161k
RG tag "L9302" is missing the the BAM header. You should have something like this in the BAM header ``` @RG ID:L9302 SM:L9302 ``` may be…
Answer: Filtering sam or bam file with maximum matching region by Pierre Lindenbaum 161k
> . Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to? samtools depth i…
Comment: Calculate Radius of Gyration [python 3] by ndm1096 • 0
Hello Franco. I am very much new with bioinformatics but I have been tasked with studying the radius of gyration of a timeseries of a prote…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
That makes a lot more sense. Thank you.
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4 by Gordon Smyth ★ 7.0k
Type ``` help("read.idat") ``` and read the example at the bottom of the page, which shows you how to set the `other$Detection` component o…
Comment: Free/open source 23andme-like analysis by swbarnes2 14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely by swbarnes2 14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely by ATpoint 81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file by swbarnes2 14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2 by Ram 43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
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