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1,000 results • Page 3 of 20
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10
votes
15
replies
1.3k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
3 months ago by Chris ▴ 200
10
votes
19
replies
2.8k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank blast UniProt
updated 2.4 years ago by 134k • written 2.4 years ago by ▴ 20
10
votes
5
replies
5.3k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 9.7 years ago by 20 • written 12.4 years ago by 2.4k
10
votes
8
replies
1.6k
views
File Format - Fasta
sequence
7.5 years ago by Gabe Anderson ▴ 10
10
votes
7
replies
3.4k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 3 months ago by 40k • written 7.5 years ago by ▴ 330
10
votes
1
reply
3.3k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq qc
updated 13 months ago by 40k • written 8.4 years ago by ★ 2.6k
10
votes
10
replies
3.5k
views
Parameter optimization STAR
RNA-Seq
5.6 years ago by XBria ▴ 90
9
votes
13
replies
3.0k
views
Python Script to map reads to reference sequence
sequence python mapping script reference sequence
4.4 years ago by Fid_o ▴ 40
9
votes
5
replies
1.1k
views
how to retrieve all proteins related to cancer
proteins
7.4 years ago by Learner ▴ 270
9
votes
7
replies
3.1k
views
Aligning Miseq With Deletions >10 Bases
alignment miseq next-gen
updated 10.2 years ago by 20 • written 10.7 years ago by 4.2k
9
votes
13
replies
1.4k
views
SNP's and Gene?
SNP gene
3.9 years ago by imgapgenomika ▴ 10
9
votes
4
replies
2.0k
views
[Code] Converte fasta/fa files to fastq
perl fastq sed fasta
updated 13 months ago by 40k • written 7.9 years ago by ★ 9.3k
9
votes
16
replies
1.6k
views
feature extraction from SNPs in R
R gene sequence SNP
4.9 years ago by bioinfo456 ▴ 150
9
votes
10
replies
3.1k
views
generation of heat map by excel data.
R excel heatmap
updated 5.3 years ago by 40k • written 5.3 years ago by ▴ 10
9
votes
27
replies
6.7k
views
How do I use Glimmer 3.02?
sequencing
updated 4.7 years ago by • 0 • written 5.5 years ago by ▴ 50
9
votes
8
replies
1.5k
views
Union of unaligned fastq reads
RNA-Seq
6.3 years ago by Jeffin Rockey ★ 1.2k
9
votes
19
replies
1.9k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.7 years ago by schlogl ▴ 150
9
votes
7
replies
884
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA ChIP nf-core ChIP-seq
updated 16 months ago by 40k • written 17 months ago by ▴ 20
9
votes
4
replies
1.2k
views
Is there any method to run tophat ?
RNA-Seq
updated 5.1 years ago by 20 • written 5.2 years ago by • 0
9
votes
12
replies
1.2k
views
Copy number variations analysis
R CNV
updated 3.8 years ago by 11k • written 3.8 years ago by ▴ 70
9
votes
6
replies
2.9k
views
Bug in JellyFish and DSK k-mer counting tool?
dsk jellyfish k-mer
6.8 years ago by scchess ▴ 630
9
votes
13
replies
14k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 3 months ago by 40k • written 5.0 years ago by ▴ 30
9
votes
7
replies
5.3k
views
fisher test with multiple samples
statistics
updated 22 months ago by 40k • written 9.2 years ago by ▴ 220
9
votes
12
replies
6.6k
views
How to align reads on reference using python?
genome sequence gene sequencing
updated 4.8 years ago by 47k • written 4.8 years ago by ▴ 10
9
votes
10
replies
1.5k
views
How to use Poisson distribution to get meaningful expression counts?
statistics rna-seq
updated 2.2 years ago by 17k • written 2.2 years ago by ▴ 510
9
votes
10
replies
5.1k
views
6 follow
Trimmomatic: Higher number of "forward only" than "reverse only" surviving reads
trimming RNA-seq
updated 3.9 years ago by ▴ 30 • written 5.1 years ago by ▴ 20
9
votes
10
replies
2.0k
views
[solved] Convert fold changes of multiple transcripts of a given gene to a single value characterising this gene
RNA-Seq
7.0 years ago by biostart ▴ 370
9
votes
13
replies
2.4k
views
qRT-PCR data analysis steps and workflow
qRT-PCR Reference genes Normalization DeltaCt FC
4.6 years ago by mohammedtoufiq91 ▴ 230
9
votes
10
replies
2.1k
views
why there is 0/0 genotyp in VCF file?
VCF GATK Variant
4.1 years ago by star ▴ 350
9
votes
14
replies
4.0k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 18 months ago by 40k • written 8.7 years ago by ▴ 70
9
votes
7
replies
3.6k
views
7 follow
Are 2 replicates per sample sufficient for RNA-seq data analysis?
RNA-Seq R Ngs
5.6 years ago by Arindam Ghosh ▴ 510
9
votes
6
replies
996
views
Genotype meaning
genotype BL21
2.2 years ago by A_heath ▴ 140
9
votes
5
replies
3.4k
views
Which bias flags to run with Salmon before DESeq2 analysis?
RNA-Seq Salmon DESeq2 Bias Flags
4.3 years ago by cameron.holman ▴ 20
9
votes
7
replies
3.4k
views
How to use Galaxy to obtain read counts from SRA files
Galaxy read count SRA file
7.0 years ago by statfa ▴ 740
9
votes
7
replies
1.7k
views
Is the sequence quality good enough?
WGS HISEQ4000 QC
5.3 years ago by BioinfGuru ★ 1.6k
9
votes
2
replies
461
views
Answer needed urgently
Deep
updated 12 months ago by ★ 25k • written 12 months ago by • 0
9
votes
2
replies
3.0k
views
GEOquery Problems to Get GEO dataset
Geoquery
7.5 years ago by Shicheng Guo ★ 9.3k
9
votes
9
replies
1.3k
views
Convert mouse amino acid location to genomic location
genome gene
4.3 years ago by L. A. Liggett ▴ 120
9
votes
3
replies
7.0k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics rna
updated 4.5 years ago by 20 • written 11.5 years ago by ▴ 380
9
votes
4
replies
22k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
6.4 years ago by ariel.balter ▴ 210
9
votes
13
replies
2.2k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
updated 2.4 years ago by 40k • written 2.5 years ago by ▴ 30
9
votes
7
replies
1.0k
views
Reference genome location
reference positions FASTA alignment genome
updated 8 months ago by ★ 1.8k • written 9 months ago by • 0
9
votes
13
replies
1.6k
views
Archeological DNA sample - how to analyze
unmapped paleogenomics archeogenomics Assembly
20 months ago by Aruna ▴ 30
9
votes
1
reply
5.8k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq macs macs2
updated 13 months ago by 40k • written 7.9 years ago by ★ 3.4k
9
votes
14
replies
2.7k
views
vcf to xls wrong columns
vcf
7.2 years ago by cristina_sabiers ▴ 110
9
votes
13
replies
2.3k
views
Reannotating a gene: Identifying translation and transcription start sites
RNA-Seq genome gene
6.7 years ago by rh5118 ▴ 40
9
votes
5
replies
427
views
Prophage prediction tool
prophage PHASTER prediction
updated 10 weeks ago by 134k • written 10 weeks ago by ▴ 140
9
votes
4
replies
1.6k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
updated 5 months ago by 40k • written 7.1 years ago by ▴ 60
9
votes
4
replies
5.3k
views
How to analyse normalized read count?
RNA-Seq R
updated 9 months ago by 40k • written 8.3 years ago by ▴ 150
9
votes
11
replies
6.3k
views
microRNA Illumina Sequencing - Very low alignment rate
sequencing Assembly RNA-Seq
updated 20 months ago by 40k • written 9.1 years ago by ▴ 90
1,000 results • Page 3 of 20
Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Recent Replies
Comment: Getting the overlap between two GTF files by Alex Reynolds 35k
What would that be?
Answer: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
@ialbert ,I am deeply immersed in the fog and request the help ,please
Comment: bedtools intersect by position & stand not working even with common regions by rfran010 ▴ 830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files by rfran010 ▴ 830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly. If it's not done alre…
Answer: vcf.gz to vcf by Mark ★ 1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names? by Jiyao Wang ▴ 340
You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow? by Mark ★ 1.3k
Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'. Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
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