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10
votes
12
replies
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The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes human housekeeping list
4.3 years ago by msimmer92 ▴ 300
10
votes
5
replies
2.3k
views
error with samtools
RNA-Seq
updated 6.3 years ago by 20 • written 6.5 years ago by ▴ 20
10
votes
3
replies
1.2k
views
how to create new file
r
updated 6.6 years ago by 130k • written 6.6 years ago by ▴ 80
10
votes
19
replies
2.6k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank blast UniProt
updated 2.1 years ago by 130k • written 2.1 years ago by ▴ 20
10
votes
10
replies
1.6k
views
Minor allele frequency
GWAS SNPs Alleles
updated 4.6 years ago by 20 • written 6.5 years ago by ▴ 410
9
votes
13
replies
2.8k
views
Python Script to map reads to reference sequence
sequence python mapping script reference sequence
4.1 years ago by Fid_o ▴ 40
9
votes
5
replies
1.0k
views
how to retrieve all proteins related to cancer
proteins
7.1 years ago by Learner ▴ 260
9
votes
7
replies
3.0k
views
Aligning Miseq With Deletions >10 Bases
alignment miseq next-gen
updated 9.9 years ago by 20 • written 10.4 years ago by 4.2k
9
votes
13
replies
1.2k
views
SNP's and Gene?
SNP gene
3.6 years ago by imgapgenomika ▴ 10
9
votes
10
replies
1.8k
views
why there is 0/0 genotyp in VCF file?
VCF GATK Variant
3.8 years ago by star ▴ 340
9
votes
7
replies
1.8k
views
Sorting BLAST output files together?
blast
7.1 years ago by zgayk ▴ 90
9
votes
27
replies
6.3k
views
How do I use Glimmer 3.02?
sequencing
updated 4.4 years ago by • 0 • written 5.2 years ago by ▴ 50
9
votes
4
replies
1.9k
views
[Code] Converte fasta/fa files to fastq
perl fastq sed fasta
updated 10 months ago by 39k • written 7.6 years ago by ★ 9.3k
9
votes
11
replies
7.0k
views
8 follow
Extremely low mapping rates with bowtie2
alignment next-gen
updated 5.6 years ago by 20 • written 5.7 years ago by ▴ 10
9
votes
16
replies
1.4k
views
feature extraction from SNPs in R
R gene sequence SNP
4.6 years ago by bioinfo456 ▴ 150
9
votes
10
replies
1.9k
views
[solved] Convert fold changes of multiple transcripts of a given gene to a single value characterising this gene
RNA-Seq
6.7 years ago by biostart ▴ 370
9
votes
13
replies
2.2k
views
qRT-PCR data analysis steps and workflow
qRT-PCR Reference genes Normalization DeltaCt FC
4.3 years ago by mohammedtoufiq91 ▴ 230
9
votes
6
replies
856
views
Genotype meaning
genotype BL21
23 months ago by A_heath ▴ 140
9
votes
4
replies
1.1k
views
Is there any method to run tophat ?
RNA-Seq
updated 4.7 years ago by 20 • written 4.9 years ago by • 0
9
votes
2
replies
398
views
Answer needed urgently
Deep
updated 8 months ago by ★ 23k • written 8 months ago by • 0
9
votes
6
replies
3.1k
views
SOAPaligner 2.21 - does it replace all Ns by Gs in reads?
Soapaligner alignment
updated 20 months ago by 39k • written 9.0 years ago by 7.8k
9
votes
10
replies
2.1k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK Whole Exome Sequencing Mutect2
2.4 years ago by kwanghoon ▴ 20
9
votes
1
reply
5.6k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq macs macs2
updated 9 months ago by 39k • written 7.6 years ago by ★ 3.4k
9
votes
2
replies
2.9k
views
GEOquery Problems to Get GEO dataset
Geoquery
7.2 years ago by Shicheng Guo ★ 9.3k
9
votes
10
replies
1.3k
views
How to use Poisson distribution to get meaningful expression counts?
statistics rna-seq
updated 22 months ago by 17k • written 22 months ago by ▴ 510
9
votes
20
replies
3.4k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard SAM
updated 11 weeks ago by 39k • written 4.8 years ago by ▴ 680
9
votes
3
replies
6.9k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics rna
updated 4.2 years ago by 20 • written 11.2 years ago by ▴ 380
9
votes
14
replies
3.8k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 14 months ago by 39k • written 8.4 years ago by ▴ 70
9
votes
13
replies
1.4k
views
Archeological DNA sample - how to analyze
unmapped paleogenomics archeogenomics Assembly
16 months ago by Aruna ▴ 30
9
votes
13
replies
2.0k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
updated 2.1 years ago by 39k • written 2.1 years ago by ▴ 30
9
votes
7
replies
1.5k
views
Is the sequence quality good enough?
WGS HISEQ4000 QC
5.0 years ago by BioinfGuru ★ 1.6k
9
votes
7
replies
857
views
Reference genome location
reference positions FASTA alignment genome
updated 5 months ago by ★ 1.6k • written 5 months ago by • 0
9
votes
4
replies
471
views
RNA seq, secreted protein
protein gene secreted
updated 5 months ago by 21k • written 6 months ago by ▴ 160
9
votes
12
replies
1.0k
views
Copy number variations analysis
R CNV
updated 3.5 years ago by 11k • written 3.5 years ago by ▴ 70
9
votes
7
replies
1.8k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression differential average R rna-seq
updated 23 months ago by ▴ 60 • written 23 months ago by ▴ 230
9
votes
16
replies
3.1k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 11 weeks ago by 39k • written 4.8 years ago by ▴ 680
9
votes
5
replies
3.1k
views
Which bias flags to run with Salmon before DESeq2 analysis?
RNA-Seq Salmon DESeq2 Bias Flags
3.9 years ago by cameron.holman ▴ 20
9
votes
7
replies
5.2k
views
fisher test with multiple samples
statistics
updated 18 months ago by 39k • written 8.9 years ago by ▴ 220
9
votes
11
replies
4.1k
views
please someone help me with running mirdeep2
software error mirdeep2 perl
6.7 years ago by fi1d18 ★ 4.2k
9
votes
17
replies
1.8k
views
Creating intergenic bam file
R genome intergenic alignment
6.8 years ago by erincyurtman • 0
9
votes
2
replies
5.0k
views
Biopython Import Error
biopython
updated 11.0 years ago by 5.0k • written 11.0 years ago by • 0
9
votes
10
replies
3.0k
views
generation of heat map by excel data.
R excel heatmap
updated 5.0 years ago by 39k • written 5.0 years ago by ▴ 10
9
votes
6
replies
2.7k
views
Bug in JellyFish and DSK k-mer counting tool?
dsk jellyfish k-mer
6.5 years ago by SmallChess ▴ 630
9
votes
9
replies
3.8k
views
ATAC-seq TSS profile plot interpretation
ATAC-seq TSS V-plot
3.5 years ago by nanoide ▴ 100
9
votes
6
replies
1.5k
views
Question about featureCounts
RNA-Seq featurecounts
updated 22 months ago by • 0 • written 3.7 years ago by ▴ 30
9
votes
7
replies
4.9k
views
How to combine a different sources of pathway database (KEGG, BioCarta) for Pathway analysis.
Pathway enrichment analysis GWAS pathway analysis
7.0 years ago by kmsh410 ▴ 40
9
votes
7
replies
3.3k
views
How to use Galaxy to obtain read counts from SRA files
Galaxy read count SRA file
6.7 years ago by statfa ▴ 720
9
votes
4
replies
21k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
6.1 years ago by ariel.balter ▴ 200
9
votes
13
replies
12k
views
Sort bam file by coordinates using samtools
sequencing next-gen gene rna-seq Tool
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 30
9
votes
13
replies
13k
views
GC Content of Fasta file --- Python Help
sequence
6.3 years ago by Patrick Brennan ▴ 50
1,000 results • Page 3 of 20
Recent Votes
Answer: Saving results from yeastgenome.org blastp search
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Answer: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
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Comment: VCF file CSQ flag by Payal ▴ 140
Its a gvcf file #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S101 S102 S103 S104 S105
Comment: CellRanger problem by GenoMax 130k
And how much memory do you have assigned for this job? Likely you do not have enough memory for this process.
Comment: VCF file CSQ flag by Ram 39k
> a g.VCF file A `.vcf` file or a `gvcf` file?
Comment: CellRanger problem by Ram 39k
What is the cellranger command you're using?
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by Yeeshouw • 0
I see, I believe I was running an older version or have missed the option, I have updated to v2.10.5 and can see this option now. Thank you…
Answer: Saving results from yeastgenome.org blastp search by GenoMax 130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38 by GenoMax 130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions by B.N. • 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions by B.N. • 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq by GenoMax 130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq by solarchan7 • 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome by Basti ★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions by ATpoint 72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
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