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684 results • Page 1 of 14
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29
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28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 15 days ago by • 0 • written 12.8 years ago by ★ 1.7k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 18 days ago by 19k • written 20 days ago by ▴ 580
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 29 days ago by 43k • written 4.6 years ago by ★ 1.4k
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 29 days ago by ▴ 10 • written 10.3 years ago by ▴ 180
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 11 days ago by 161k • written 5.8 years ago by ▴ 180
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 21 days ago by ★ 2.5k • written 10 weeks ago by • 0
7
votes
16
replies
955
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
19 days ago by Ruqaiya • 0
1
vote
16
replies
683
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
updated 32 minutes ago by 142k • written 2 days ago by • 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 14 days ago by ★ 7.2k • written 5 months ago by ▴ 10
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 4 days ago by • 0 • written 4.8 years ago by ▴ 60
1
vote
14
replies
2.5k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 15 days ago by 142k • written 4.5 years ago by ▴ 20
10
votes
14
replies
790
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 11 days ago by 142k • written 16 days ago by • 0
13
votes
14
replies
949
views
High Malat-1 expression in single cell data
single-cell
updated 10 days ago by ▴ 40 • written 19 days ago by ▴ 40
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 7 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 24 days ago by • 0 • written 2.3 years ago by ▴ 10
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 15 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 23 hours ago by ▴ 170 • written 7.1 years ago by ▴ 240
11
votes
12
replies
1.2k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 29 days ago by 43k • written 29 days ago by • 0
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 29 days ago by • 0 • written 12.1 years ago by ★ 2.9k
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 9 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
2
votes
11
replies
677
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
1 day ago by egascon • 0
0
votes
11
replies
716
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
22 days ago by atowns21 • 0
1
vote
11
replies
5.6k
views
Truncated Bam Error
R next-gen sequencing software error
updated 12 days ago by • 0 • written 6.2 years ago by ▴ 20
0
votes
11
replies
545
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
5 days ago by Tuck898 • 0
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 19 days ago by ★ 1.2k • written 4 weeks ago by • 0
4
votes
11
replies
888
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 24 days ago by 4.2k • written 25 days 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 22 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
0
votes
10
replies
641
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 18 days ago by 19k • written 26 days ago by • 0
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 29 days ago by 43k • written 4.6 years ago by ▴ 140
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 18 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
1
vote
10
replies
892
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 12 days ago by • 0 • written 4 months ago by ▴ 30
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
23 days ago by DKA ▴ 40
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 15 days ago by • 0 • written 2.2 years ago by • 0
3
votes
9
replies
623
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 24 days ago by 100k • written 25 days ago by • 0
2
votes
9
replies
942
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 24 days ago by 4.2k • written 7 months ago by • 0
0
votes
9
replies
610
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 3 days ago by ★ 2.0k • written 11 days ago by ▴ 140
0
votes
9
replies
352
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
2 days ago by njornet ▴ 20
1
vote
9
replies
403
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 8 days ago by 19k • written 11 days ago by ★ 1.8k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
18 days ago by anna ▴ 20
0
votes
9
replies
602
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
2 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 19 days ago by 43k • written 9 months ago by • 0
2
votes
9
replies
707
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 3 days ago by 161k • written 10 days ago by • 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 9 days ago by • 0 • written 5.8 years ago by ▴ 30
4
votes
9
replies
427
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
1 day ago by Gabriel R. ★ 2.9k
3
votes
8
replies
690
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 11 days ago by ▴ 410 • written 15 days ago by ▴ 100
0
votes
8
replies
462
views
Different output for read length
samtools BAM
8 days ago by marco.barr ▴ 130
3
votes
8
replies
604
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
11 days ago by Qroid ▴ 40
2
votes
8
replies
385
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 6 days ago by 161k • written 6 days ago by ▴ 100
0
votes
8
replies
534
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 17 days ago by 4.2k • written 19 days ago by ▴ 10
1
vote
8
replies
555
views
Downsampling fastq file
downsample fastq
17 days ago by marco.barr ▴ 130
684 results • Page 1 of 14
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the bug by removing nucmer threading flag "**-t**" from line#16 of psvcp_v1.01-main script "**Refgenome_update_by_quest.sh"**.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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