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900 results • Page 2 of 18
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7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed coverage gene
updated 3 days ago by 38k • written 16 months ago by ▴ 10
0
votes
6
replies
3.2k
views
How To Download Genbank Files For Some Organism Using Biojava Utilities
genbank
updated 22 days ago by 38k • written 9.0 years ago by ▴ 20
5
votes
6
replies
434
views
I can not allocate ram memory for WSL2
WSL2
11 days ago by ailton • 0
0
votes
6
replies
732
views
cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
bcl2fastq cellranger-arc mkfastq cellranger
updated 12 days ago by ▴ 10 • written 7 weeks ago by • 0
0
votes
6
replies
1.9k
views
Getting matrix of QDs from VCF file
vcf snp
updated 18 days ago by • 0 • written 6.4 years ago by ▴ 510
0
votes
6
replies
446
views
Recreating a SPAdes Assembly
fasta SPAdes Assembly BAM
updated 8 days ago by 38k • written 4 weeks ago by • 0
5
votes
6
replies
2.9k
views
Changes log2FC values of DESeq2
log2FC DESeq2
updated 2 days ago by 38k • written 5.3 years ago by ▴ 30
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services java
updated 4 days ago by 38k • written 7.8 years ago by ▴ 170
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure splign
updated 4 days ago by 38k • written 6.4 years ago by ▴ 160
1
vote
6
replies
1.0k
views
gff file
GFF UNIPRTOT
updated 3 days ago by 38k • written 18 months ago by ▴ 10
5
votes
6
replies
621
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
mates bed bam samtools
12 days ago by Eliveri ▴ 340
0
votes
6
replies
482
views
Issue in import files in Metaboanalyst
Metaboanalyst R
updated 8 days ago by 38k • written 6 weeks ago by ▴ 10
6
votes
6
replies
3.5k
views
Already Working In The Field Of Bioinformatics With A Bachelors, Is A Masters Degree Worth The Time?
masters career
updated 25 days ago by 38k • written 9.5 years ago by ▴ 30
2
votes
6
replies
303
views
bioinformatics problems solved by graphs data structure
Graph algorithm data-structure
updated 2 days ago by 38k • written 2 days ago by • 0
6
votes
6
replies
910
views
RNA-seq pipeline for degraded RNA
RNA-Seq degraded pipeline alignment
updated 19 days ago by ▴ 80 • written 2.2 years ago by ▴ 60
2
votes
6
replies
1.0k
views
GFF3 TO GTF CONVERSION
GFF3 Hydra GFF GTF
updated 4 days ago by 38k • written 14 months ago by • 0
0
votes
6
replies
420
views
WGCNA goodGenes message error
goodGenes WGCNA
updated 16 days ago by 3.1k • written 24 days ago by • 0
3
votes
6
replies
4.3k
views
Why Do I Get A Makeblastdb Error: File Does Not Match Input Format Type, Default Input Type Is Fasta
genomics blast-plus
updated 24 days ago by 38k • written 9.3 years ago by ▴ 120
0
votes
6
replies
1.1k
views
Raw data for chromosome 21
WCS bam sequencing
updated 3 days ago by 38k • written 4.0 years ago by • 0
1
vote
6
replies
950
views
problem for comparing 2 type of annotation file
gencode RNA-Seq TCGA
updated 2 days ago by ▴ 750 • written 4.8 years ago by ▴ 160
2
votes
6
replies
327
views
Genes in 10x don't match genes in ENSBL
gene_mapping bioconductor singleCellRNAseq
updated 15 days ago by ★ 1.0k • written 16 days ago by ▴ 10
0
votes
5
replies
460
views
Should I use TPM or TMM to plot gene expression boxplots in RNAseq?
RNASeq TMM DEG TPM DESeq2
updated 23 days ago by 16k • written 24 days ago by ▴ 80
0
votes
5
replies
836
views
Problems with consensus fasta
bed bcftools samtools
updated 3 days ago by 38k • written 15 months ago by ▴ 80
2
votes
5
replies
2.3k
views
How to get gseKEGG() to accept an input gene list?
clusterprofiler dose gene-enrichment-analysis R
updated 24 days ago by ▴ 20 • written 20 months ago by ▴ 20
0
votes
5
replies
649
views
AnalysingTopHat and Fast QC results
tophat FastQC RNA-seq
updated 8 days ago by 38k • written 21 months ago by • 0
1
vote
5
replies
551
views
bwa-meth unrecognized reference name during sam_parse
EM-seq Methyl-seq alignment bwa-meth
11 days ago by bp22 ▴ 30
0
votes
5
replies
948
views
Problem with normalization by bcftools
vcf bcftools samtools
updated 3 days ago by 38k • written 2.9 years ago by ▴ 20
1
vote
5
replies
317
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R row_split ComplexHeatmap
updated 4 days ago by ▴ 710 • written 4 days ago by • 0
0
votes
5
replies
1.7k
views
What is the difference between using "-f 0.5 -r" and "-f 0.5 -F 0.5" in bedtools intersect?
bedtools intersect
updated 12 days ago by 38k • written 6.8 years ago by • 0
1
vote
5
replies
1.7k
views
How to make bed file of TSS (approximately 2kb, 1 kb upstream and 1kb downstream) of genes
RNA-Seq
updated 12 days ago by 38k • written 2.7 years ago by • 0
0
votes
5
replies
322
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq scRNA-seq single-cell genomics ngs
updated 4 days ago by 127k • written 5 days ago by ▴ 650
0
votes
5
replies
490
views
BAM file became smaller after merging
BAM
updated 4 days ago by 38k • written 11 months ago by • 0
0
votes
5
replies
2.5k
views
Recoding plink file from 12 to 01
plink plink2chromopaiter.pl
updated 2 days ago by 38k • written 5.2 years ago by ▴ 20
0
votes
5
replies
1.7k
views
Analyzing .fasta file.
fasta protein-evolution phylogenetic-tree
updated 8 days ago by 38k • written 4.9 years ago by ▴ 110
3
votes
5
replies
1.9k
views
Cellranger count command for single end fastq
RNA-Seq sequencing
updated 25 days ago by 38k • written 2.3 years ago by ▴ 40
1
vote
5
replies
692
views
Read count using htseq-count.
Assembly RNA-Seq gene
updated 12 days ago by 38k • written 2.0 years ago by • 0
3
votes
5
replies
1.7k
views
htseq counts to make matrix in Rstudio
RNA-Seq
updated 16 days ago by 38k • written 2.6 years ago by • 0
1
vote
5
replies
1.2k
views
Star index generation - 'std::bad_alloc' error
STAR
updated 5 days ago by 38k • written 2.2 years ago by • 0
0
votes
5
replies
1.7k
views
Need Bioinformatics Help - Analyzing Unknown Dna Sequence
gene sequence Nucleotide
updated 8 days ago by 38k • written 4.4 years ago by • 0
1
vote
5
replies
4.9k
views
How To Find The Total Number Of Reads Used By Trinity Assembler To Perform Assembly
trinity RNA-seq
updated 23 days ago by 38k • written 9.2 years ago by ▴ 50
1
vote
5
replies
1.5k
views
Post alignment using RseQC
alignment RNA-Seq RSeQC
updated 2 days ago by 38k • written 5.5 years ago by ▴ 570
0
votes
5
replies
780
views
Inquiry related to vcf file and formatting
vcf bcftools
updated 3 days ago by 38k • written 19 months ago by ▴ 140
1
vote
5
replies
1.8k
views
igv_plotter error, I cannot run igv_plotter on my BAM file, RuntimeError: Xvfb did not start
visualisation bam igv_plotter igv
updated 3 days ago by 38k • written 5.7 years ago by ▴ 350
14
votes
5
replies
2.7k
views
bioinformatics basic training
genome
updated 12 days ago by 38k • written 8.3 years ago by • 0
2
votes
5
replies
551
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 4 days ago by 13k • written 8 days ago by ▴ 30
1
vote
5
replies
528
views
BWA-mem not working with Snakemake + singularity
snakemake bwa singularity
18 days ago by brunobsouzaa ▴ 810
0
votes
5
replies
371
views
ANNOVAR is not reading input data
ANNOVAR
updated 26 days ago by 38k • written 4 weeks ago by ▴ 10
0
votes
5
replies
3.7k
views
reading CELfiles for Human Exon 1.0 ST Array [CDF: HuEx-1_0-st-v2,coreR3,A20071112,EP]
CEL RNA-Seq software-error R
updated 3 days ago by 38k • written 6.8 years ago by ▴ 30
4
votes
5
replies
520
views
Need help to perform survival analysis
survival analysis mirna
updated 13 days ago by ★ 23k • written 14 days ago by • 0
0
votes
5
replies
937
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq normalization batcheffect single_cell_features training_test_split
19 days ago by mmitra ▴ 60
900 results • Page 2 of 18
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downloading human gene symbol with duplicates
downloading human gene symbol with duplicates
Answer: How to make cut off linein cluster,
How to make cut off linein cluster,
Answer: GetBM - GERP conservation score for GRCm39
Answer: Using STAR for RNA seq-alignment.
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Recent Replies
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by Adaline.D • 0
That explains a lot to me. Thank you, seidel! They used Affymetrix Human Gene 1.0 ST Array chips. Hope you have a wonderful day.
Comment: How to make cut off linein cluster, by Info.shi ▴ 20
Thank you so much it worked. I highly appreciate your help.
Answer: How to make cut off linein cluster, by Jeremy ▴ 770
Try adding the following line of code: abline(h = .02)
Comment: Problem with fatsq-dump by Utpal • 0
Thank you for your support. I tried the command conda install -c bioconda sra-tools But, still with the command, fastq-dump it return…
Comment: RNA Sequencing and Vg pan -transcriptome build by Jordan M Eizenga ▴ 70
The `vg mpmap` subcommand has features for mapping RNA-seq data to a graph. We describe in more detail in [this publication][1], including …
Comment: how to import hdf5 Hi-C data into R using HiTC package by rpolicastro 11k
From the error you may need to specify the file path instead of passing it the imported data.
Comment: RNA Sequencing and Vg pan -transcriptome build by cmdcolin ★ 2.9k
i am not sure how about the data input format but 'hisat2' is able to 'align rna-seq to a population reference'. this may be a little diffe…
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by seidel 11k
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, y…
Comment: Log2 FC Threshold by seidel 11k
Given that 0.2 is a 1.15 fold change (2^0.2) you're right to be skeptical, but there's no clear answer as to the significance. Consider tha…
Comment: Read lengths greater than insert length by GenoMax 127k
As I said above the adapters are each ~60 bp long so they add ~120 bp (5' and 3' end adapters) to the length of the DNA fragment. What you …
Comment: Problem with fatsq-dump by GenoMax 127k
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139 At least the program seems to be ins…
Comment: Read lengths greater than insert length by shpak.max ▴ 30
I'm not claiming that all fragment lengths are exactly 50, the typical range for my data is 45-60. However, my read lengths are all 150, so…
Answer: Read lengths greater than insert length by GenoMax 127k
Illumina libraries are made by adding adapters to the ends of DNA fragment(s). Those adapters themselves are about 60 nucleotides long. Not…
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang by Rob 5.9k
If you have the raw data, you can easily get this information using [alevin-fry](https://www.nature.com/articles/s41592-022-01408-3). It pr…
Answer: Matching gene-expression data with clinical data: best practices. by pilargmarch ▴ 60
I really like using [the R/Bioconductor package TCGAbiolinks][1], it gives you clinical and expression data by patient ID. [1]: http…
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