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182 results • Page 1 of 4
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76
votes
72
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
3 days ago by Kevin Blighe 87k
8
votes
16
replies
869
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 2 days ago by ★ 2.4k • written 7 weeks ago by • 0
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 4 days ago by • 0 • written 2.2 years ago by ▴ 10
25
votes
11
replies
3.7k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 4 days ago by 43k • written 14.6 years ago by 100k
0
votes
11
replies
517
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
2 days ago by atowns21 • 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 2 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
4
votes
11
replies
666
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 4 days ago by 4.2k • written 5 days ago by • 0
1
vote
10
replies
938
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
3 days ago by DKA ▴ 40
2
votes
9
replies
846
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 4 days ago by 4.2k • written 6 months ago by • 0
3
votes
9
replies
456
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 4 days ago by 100k • written 5 days ago by • 0
0
votes
9
replies
256
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
updated 3 hours ago by 141k • written 15 hours ago by • 0
4
votes
8
replies
543
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 1 day ago by 35k • written 2 days ago by ▴ 10
1
vote
8
replies
806
views
Adding CB tag to bam file
samtools bam
updated 3 days ago by 161k • written 9 days ago by • 0
0
votes
8
replies
335
views
Error in cnetplot enrichplot package
R
updated 5 days ago by 43k • written 5 days ago by • 0
8
votes
8
replies
646
views
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 5 hours ago by 8.3k • written 23 hours ago by ▴ 530
8
votes
8
replies
580
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 3 days ago by 14k • written 4 days ago by ▴ 10
1
vote
7
replies
382
views
gvcf joint calling
WES GATK VCF gVCF
10 hours ago by zihanss • 0
4
votes
7
replies
456
views
To get p-values for the TPM
P-value TPM RSEM
updated 3 days ago by ★ 5.9k • written 4 days ago by • 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 3 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
0
votes
7
replies
328
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 2 days ago by 141k • written 6 days ago by • 0
4
votes
7
replies
603
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 1 day ago by ★ 5.9k • written 5 days ago by ▴ 10
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 10 hours ago by 43k • written 8 months ago by ▴ 10
1
vote
6
replies
387
views
ScRNA data question
scRNA Vlnplot Samples
1 day ago by starswillfade ▴ 10
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 1 day ago by 43k • written 2.4 years ago by ▴ 10
0
votes
6
replies
440
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 4 days ago by • 0 • written 27 days ago by ▴ 20
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 2 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
0
votes
6
replies
326
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
4 days ago by Sd • 0
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 2 days ago by 82k • written 3.9 years ago by ▴ 280
3
votes
6
replies
661
views
Ciriquant not configuring hisat2 indexed files
ciriquant
6 days ago by Atul K. • 0
0
votes
5
replies
326
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 3 days ago by 141k • written 4 days ago by ▴ 90
1
vote
5
replies
284
views
Downsampling fastq file
downsample fastq
updated 6 days ago by 43k • written 6 days ago by ▴ 80
0
votes
5
replies
322
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 1 day ago by 100k • written 4 days ago by ▴ 10
8
votes
5
replies
5.4k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
2
votes
5
replies
458
views
Marking duplicates using UMIs
Deduplication UMI
updated 6 days ago by 19k • written 7 days ago by • 0
2
votes
5
replies
304
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
2 days ago by Lada ▴ 30
1
vote
5
replies
603
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 5 days ago by • 0 • written 3 months ago by • 0
3
votes
5
replies
279
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
5
replies
319
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
4 days ago by njornet ▴ 20
1
vote
5
replies
349
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
5 days ago by anasjamshed ▴ 120
3
votes
5
replies
554
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
6 days ago by n_navy • 0
2
votes
5
replies
324
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
12 minutes ago by ashaneev07 ▴ 20
2
votes
4
replies
308
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 4 days ago by 14k • written 5 days ago by • 0
3
votes
4
replies
669
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
6 days ago by rahu • 0
4
votes
4
replies
386
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 1 day ago by ★ 1.7k • written 3 days ago by ★ 3.9k
2
votes
4
replies
285
views
interpretartion of a vcf file
calling genotype ONT variant diploid
4 days ago by samuelkalandarov2002 ▴ 10
5
votes
4
replies
641
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
4 days ago by kirillkirilenko ▴ 40
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 3 days ago by • 0 • written 2.4 years ago by • 0
1
vote
4
replies
431
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 4 days ago by • 0 • written 5 months ago by • 0
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 3 days ago by • 0 • written 8.3 years ago by • 0
2
votes
4
replies
321
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
4 days ago by HyperEvo • 0
182 results • Page 1 of 4
Recent Votes
Batch effects : ComBat or removebatcheffects (limma package) ?
How to input margin to UpsetR figure
Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
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Recent Replies
Answer: Fetch table from clinvar database according to a list of rsid by ashaneev07 ▴ 20
Hii... i have updated the script in python..But, still getting no data found. Actually the data is there, i have print the parsed html file…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
Comment: Downloading full alignments from Pfam by GenoMax 141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.3k
While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
1. What does clipped Fastq mean? both forward and reverse reads in the same file? 2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right? I'l try spades. [1]: http…
Comment: How to assign cell types after integration in scRNA by Francesco ▴ 10
Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
Answer: Can I run cellassign on samples independently if there is batch effect present? by Francesco ▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling by zihanss • 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted? by ATpoint 82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
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