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1,000 results • Page 4 of 20
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7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 10 months ago by 43k • written 3.9 years ago by ▴ 60
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
11 months ago by eesha28112001 • 0
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 10 months ago by 43k • written 9.5 years ago by • 0
1
vote
8
replies
2.5k
views
subset data problem
R seurat
9 months ago by Andy ▴ 120
0
votes
8
replies
1.5k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools MarkDuplicates
updated 7 weeks ago by • 0 • written 19 months ago by • 0
1
vote
8
replies
1.5k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count cellranger cite-seq scRNA-seq
updated 4 months ago by 82k • written 9 months ago by ★ 1.8k
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython python
updated 11 months ago by 43k • written 4.4 years ago by • 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 24 days ago by 43k • written 6.5 years ago by ★ 1.6k
0
votes
8
replies
4.5k
views
Downloading single cell data from NCBI
ncbi rna-seq fastq-dump single-cell
updated 8 months ago by 43k • written 5.4 years ago by ▴ 380
5
votes
8
replies
615
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by 6.4k • written 3 months ago by ▴ 50
0
votes
8
replies
1.0k
views
The inchworm process failed. Trinity running error.
inchworm transcriptome trinity
updated 11 months ago by 142k • written 11 months ago by • 0
0
votes
8
replies
662
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 9 weeks ago by ▴ 10 • written 3 months ago by ▴ 30
3
votes
8
replies
918
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 142k • written 10 months ago by • 0
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic rna-seq trinity
updated 8 months ago by 43k • written 8.0 years ago by ▴ 110
1
vote
8
replies
452
views
Downsampling fastq file
downsample fastq
3 days ago by marco.barr ▴ 90
1
vote
8
replies
992
views
Reads in IGV are mostly in intron regions
Patchseq RNA-seq
10 months ago by Kai_Qi ▴ 130
1
vote
8
replies
1.1k
views
How does one access TCGA controlled data in AWS S3?
tcga aws
updated 6 months ago by ★ 1.2k • written 6 months ago by ▴ 10
2
votes
8
replies
699
views
TCGA Biospecimens Slides Extraction
tcga
updated 10 weeks ago by ★ 1.2k • written 11 weeks ago by ▴ 10
0
votes
8
replies
373
views
Error in cnetplot enrichplot package
R
updated 10 days ago by 43k • written 10 days ago by • 0
4
votes
8
replies
614
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
2
votes
8
replies
1.0k
views
VCF file CSQ flag
vcf exome-sequencing
updated 10 months ago by 43k • written 11 months ago by ▴ 160
1
vote
8
replies
1.1k
views
Shannon's Entropy by Sliding Window in R
Sequence Window R Entropy Sliding
updated 11 months ago by ▴ 850 • written 17 months ago by • 0
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda gatk
10 months ago by bestone ▴ 30
0
votes
8
replies
1.5k
views
VCF samtools
vcf samtools variant-calling
updated 10 months ago by 43k • written 2.4 years ago by • 0
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 11 months ago by 43k • written 4.6 years ago by ▴ 120
1
vote
8
replies
1.3k
views
Betacoronavirus.00.nsq error
biostars-handbook corona
updated 10 months ago by 43k • written 2.3 years ago by • 0
0
votes
8
replies
1.2k
views
BAM header edit with a list of amplicons
samtools BAM
updated 10 months ago by 43k • written 2.3 years ago by • 0
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 15 months ago by • 0
4
votes
8
replies
1.9k
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 3 months ago by ★ 16k • written 3 months ago by • 0
3
votes
8
replies
636
views
Huge decrease of BUS records using bustools
single-cell bustools 10X
9 weeks ago by julien.wollbrett • 0
0
votes
8
replies
573
views
STAR aligner options
STAR
5 weeks ago by theophile • 0
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST R
updated 11 weeks ago by ▴ 140 • written 2.7 years ago by ▴ 20
5
votes
7
replies
844
views
About the value in bigwig file
ATAC-seq
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 260
3
votes
7
replies
2.2k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance RNA-SEQ RSEM Trinity
updated 11 months ago by 43k • written 2.6 years ago by ▴ 60
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 0
0
votes
7
replies
530
views
SNP calling with many samples using bcftools
bcftools SNP multithreading
5 months ago by George ▴ 10
3
votes
7
replies
1.0k
views
IGV not showing bigwig track information
bigwig IGV ChIP-seq
updated 5 months ago by 82k • written 5 months ago by ▴ 10
1
vote
7
replies
1.6k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto STAR RNA-seq Transcript_variants
11 months ago by sohail.mbio • 0
0
votes
7
replies
1.4k
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
snakemake sra-tools SRA
updated 10 months ago by 43k • written 12 months ago by ▴ 80
2
votes
7
replies
567
views
Need a link to OLDERADO server
pdb protein nmr structure
7 weeks ago by b2003 • 0
1
vote
7
replies
1.2k
views
For loop STAR not working
RNA-Seq STAR
updated 10 months ago by 43k • written 2.9 years ago by ▴ 30
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.1 years ago by ▴ 70
0
votes
7
replies
390
views
single nuclei sequencing questions
fastq single-nuclei-sequencing
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
4
votes
7
replies
582
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 19 days ago by 43k • written 20 days ago by ▴ 20
0
votes
7
replies
4.4k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq alignment software-error next-gen sequence
updated 4 months ago by 43k • written 6.0 years ago by • 0
2
votes
7
replies
1.1k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean error
updated 8 months ago by 142k • written 8 months ago by • 0
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr fold-change
updated 7 months ago by 43k • written 5.9 years ago by ▴ 80
1
vote
7
replies
861
views
Ribosomal cluster
seurat single-cell
6 months ago by Chris ▴ 260
0
votes
7
replies
451
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 5 weeks ago by 142k • written 5 weeks ago by • 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 24 days ago by 43k • written 6.5 years ago by ▴ 10
1,000 results • Page 4 of 20
Recent Votes
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
Answer: Does comparing two different groups to a common third group introduce bias in th
Comment: High Malat-1 expression in single cell data
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Recent Replies
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file by GenoMax 142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme by e.r.zakiev ▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ by GenoMax 142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie by GenoMax 142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
Comment: High Malat-1 expression in single cell data by dsull ★ 6.0k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data by carolofharvest ▴ 30
Thank you for sharing. What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
Comment: Do I need to go back and filter my long-reads? by GenoMax 142k
> I think I will filter the reads ultimately. If your data was not run and basecalled using the same exact version of pore/software for a…
Comment: Raw counts using stringtie by Ram 43k
What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
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