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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
1
vote
8
replies
1.1k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
5 months ago by nick_b55 ▴ 10
2
votes
8
replies
994
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 9 weeks ago by ▴ 560 • written 4 months ago by 4.2k
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
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
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
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
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
1
vote
8
replies
843
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq deseq2
5 months ago by pingu77 ▴ 20
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 1 day ago by • 0 • written 5.1 years ago by 11k
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 11 months ago by 43k • written 12 months ago by ▴ 30
3
votes
8
replies
919
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 142k • written 10 months ago by • 0
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
1
vote
8
replies
993
views
Reads in IGV are mostly in intron regions
Patchseq RNA-seq
10 months ago by Kai_Qi ▴ 130
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
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq NGS RNA-Seq
3 months ago by subhiksha ▴ 30
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
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 16 days ago by 43k • written 7.0 years ago by ▴ 20
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 24 days ago by • 0 • written 4.7 years ago by ▴ 180
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
Using NCBIs EDirect to download pubmed abstract
edirect pubmed NCBI
updated 10 months ago by 43k • written 5.9 years ago by • 0
0
votes
8
replies
663
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
1
vote
8
replies
2.5k
views
subset data problem
R seurat
9 months ago by Andy ▴ 120
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
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
2.9k
views
How to convert a database from protein to nucleotide
blastn unix blastx blast
updated 11 months ago by 43k • written 7.1 years ago by • 0
3
votes
8
replies
2.0k
views
Kallisto mapping paired end
Kallisto mapping
updated 11 months ago by 43k • written 2.2 years ago by ▴ 20
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
3
votes
8
replies
1.0k
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST bowtie2 BWA alignment
8 months ago by cheesefish21 ▴ 10
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
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
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
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
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
0
votes
7
replies
590
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
10 weeks ago by sacryt • 0
0
votes
7
replies
927
views
SNPeff problem
snpEff
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
7
replies
3.8k
views
MUMmer plot visualization
MUMmer plot
updated 11 weeks ago by • 0 • written 3.2 years ago by ▴ 90
0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf dna vcf ensembl ngs
updated 5 months ago by • 0 • written 15 months ago by ▴ 30
6
votes
7
replies
1.7k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 11 months ago by 43k • written 6.9 years ago by ▴ 90
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
5
votes
7
replies
961
views
Salmon index not progressing
salmon
updated 7 months ago by 54k • written 7 months ago by ▴ 160
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
1
vote
7
replies
910
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 5 weeks ago by 43k • written 9 months ago by ▴ 100
1
vote
7
replies
892
views
help with weird PCA? (vcfR)
vcftools vcfR R
5 months ago by MaeBH • 0
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
0
votes
7
replies
712
views
create an all against all fasta file
python fasta
updated 6 months ago by 43k • written 6 months ago by • 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
1
vote
7
replies
921
views
Filtering a 10X generated .bam file based on a list of barcodes
snRNA-seq scRNA-seq samtools BAM RNA-seq
6 months ago by jhnicolas • 0
1
vote
7
replies
865
views
Ribosomal cluster
seurat single-cell
6 months ago by Chris ▴ 260
0
votes
7
replies
964
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 5 months ago by 43k • written 5 months ago by ▴ 10
1,000 results • Page 4 of 20
Recent Votes
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
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Popular Question to Thanujay S • 0
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Recent Replies
Comment: Segmentation error while using a tool by Thanujay S • 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA by Thanujay S • 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool by Ruqaiya • 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2 by GenoMax 142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download by GenoMax 142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified. by GenoMax 142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis by Gordon Smyth ★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon. by lcordeiro ▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome by chrchang523 10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file? by chrchang523 10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA by bk11 ★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R by Erina • 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by swbarnes2 14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Mbofire • 0
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