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699 results • Page 1 of 14
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76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
27 days ago by Kevin Blighe 88k
29
votes
28
replies
35k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 20 days ago by • 0 • written 12.8 years ago by ★ 1.7k
39
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 22 days ago by 19k • written 25 days ago by ▴ 590
9
votes
23
replies
9.9k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
11 days ago by vytarasov ▴ 180
13
votes
18
replies
6.2k
views
9 follow
Blastn, need help to increase speed
RNA-Seq blastn blast+
updated 15 hours ago by ★ 2.5k • written 3.2 years ago by ▴ 20
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 26 days ago by ★ 2.5k • written 11 weeks ago by • 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 15 days ago by 162k • written 5.8 years ago by ▴ 180
1
vote
16
replies
799
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
updated 4 days ago by 142k • written 7 days ago by • 0
7
votes
16
replies
996
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
23 days ago by Ruqaiya • 0
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 18 days ago by ★ 7.2k • written 5 months ago by ▴ 10
19
votes
15
replies
2.3k
views
Forum: What is the amount of sequencing data produced annually?
data research sequencing
updated 1 day ago by • 0 • written 8 months ago by ▴ 70
13
votes
14
replies
1.0k
views
High Malat-1 expression in single cell data
single-cell
updated 14 days ago by ▴ 40 • written 23 days ago by ▴ 40
1
vote
14
replies
2.5k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 20 days ago by 142k • written 4.5 years ago by ▴ 20
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 8 days ago by ▴ 10 • written 4.9 years ago by ▴ 60
10
votes
14
replies
841
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 15 days ago by 142k • written 21 days ago by • 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 2 days ago by ▴ 30 • written 3.1 years ago by • 0
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 12 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
0
votes
13
replies
3.7k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 28 days ago by • 0 • written 2.3 years ago by ▴ 10
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 13 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 19 days ago by ▴ 10 • written 3.2 years ago by ▴ 120
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 5 days ago by ▴ 170 • written 7.1 years ago by ▴ 240
0
votes
11
replies
590
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
10 days ago by Tuck898 • 0
4
votes
11
replies
916
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 28 days ago by 4.2k • written 29 days ago by • 0
25
votes
11
replies
3.8k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 29 days ago by 44k • written 14.7 years ago by 100k
1
vote
11
replies
5.6k
views
Truncated Bam Error
R next-gen sequencing software error
updated 16 days ago by • 0 • written 6.2 years ago by ▴ 20
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 23 days ago by ★ 1.2k • written 5 weeks ago by • 0
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 26 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
2
votes
11
replies
781
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
5 days ago by egascon • 0
0
votes
11
replies
743
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
27 days ago by atowns21 • 0
4
votes
11
replies
924
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
22 hours ago by J ▴ 10
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 23 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 2 days ago by 44k • written 5 months ago by 4.2k
1
vote
10
replies
916
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 16 days ago by • 0 • written 4 months ago by ▴ 30
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by ▴ 590
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
28 days ago by DKA ▴ 40
0
votes
10
replies
663
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 22 days ago by 19k • written 4 weeks ago by • 0
1
vote
10
replies
587
views
Add stats to the plot
R
16 hours ago by Ghada • 0
1
vote
9
replies
470
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 12 days ago by 19k • written 15 days ago by ★ 1.8k
2
votes
9
replies
778
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 7 days ago by 162k • written 15 days ago by • 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 14 days ago by • 0 • written 5.8 years ago by ▴ 30
0
votes
9
replies
620
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
7 days ago by Arton ▴ 10
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 23 days ago by 44k • written 9 months ago by • 0
0
votes
9
replies
683
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 7 days ago by ★ 2.0k • written 16 days ago by ▴ 140
3
votes
9
replies
659
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 28 days ago by 100k • written 4 weeks ago by • 0
2
votes
9
replies
965
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 28 days ago by 4.2k • written 7 months ago by • 0
0
votes
9
replies
400
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
6 days ago by njornet ▴ 20
4
votes
9
replies
524
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
5 days ago by Gabriel R. ★ 2.9k
4
votes
9
replies
646
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 1 day ago by ▴ 130 • written 7 days ago by ▴ 20
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 19 days ago by • 0 • written 2.2 years ago by • 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
23 days ago by anna ▴ 20
699 results • Page 1 of 14
Recent Votes
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
C: Reads mapped to another chromosome in paired-end data of RNA-seq
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Recent Replies
Comment: Mouse or Rat Gene Expression Data Similar to GTEx by GenoMax 142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx by GenoMax 142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx by bk11 ★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files by a.penatauber • 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq by ATpoint 82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows by reza ▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP by Pierre Lindenbaum 162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows by Pierre Lindenbaum 162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows by reza ▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
Answer: merge overlaps and remove non overlap genomic windows by Pierre Lindenbaum 162k
> have two bed files these are not bed files. A chromosome is missing in chromosome 1 > How can I create a file from the two mention…
Comment: Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq) by GenoMax 142k
Have you checked for presence of rRNA in the affected samples? That can be one possibility for these peaks. In theory if you are aligning …
Comment: Allele count of 2 for homoplasmic MT variants in VCF by GenoMax 142k
Please accept the answer (green check mark) to provide closure to this thread.
Comment: Trimmomatic running but files containing purged reads are empty by GenoMax 142k
Perhaps there were no low quality reads either.
Comment: Allele count of 2 for homoplasmic MT variants in VCF by Arton ▴ 10
Thank you for the helpful answer!
Comment: How to get the ratio of allele counts from GATK derived VCF file? by DBScan ▴ 300
I think GATK only counts informative reads in AD, do you have a DP field? DP should be closer what FreeBayes reports. You can also check GA…
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