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197 results • Page 4 of 4
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3
votes
5
replies
340
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
5 days ago by Maverick ▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 6 days ago by • 0 • written 5.1 years ago by 11k
0
votes
2
replies
203
views
Base Quality Score Recalibration with different reference genome
SNPs GATK BQSR RNA-seq
6 days ago by dtnondorf • 0
1
vote
7
replies
530
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 1 day ago by ▴ 400 • written 6 days ago by ▴ 90
1
vote
2
replies
246
views
RNA-seq data for deep learning classification
rna-seq
6 days ago by yahn • 0
3
votes
8
replies
520
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
2 days ago by Qroid ▴ 40
0
votes
1
reply
158
views
Provean help
variant Provean
updated 6 days ago by ★ 27k • written 7 days ago by • 0
0
votes
6
replies
314
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
updated 6 days ago by ★ 6.0k • written 7 days ago by • 0
1
vote
7
replies
457
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
6 days ago by eebloom ▴ 80
3
votes
3
replies
337
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 6 days ago by 82k • written 7 days ago by • 0
10
votes
14
replies
656
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 2 days ago by 142k • written 8 days ago by • 0
1
vote
3
replies
247
views
Odd alignment question/finding
Alignment
updated 6 days ago by ★ 2.1k • written 7 days ago by • 0
0
votes
7
replies
573
views
Post-imputation plot
michigan-imputation-server quality-control
updated 6 days ago by 3.9k • written 10 days ago by ▴ 10
1
vote
3
replies
292
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart plant ensembl
3 days ago by Dora ▴ 10
0
votes
2
replies
231
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
2 days ago by Ahiad Chen Zion • 0
1
vote
5
replies
345
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
6 days ago by Riccardo ▴ 10
3
votes
3
replies
230
views
Gene Specific coverage from WGS data
linux WGS Bioinformatics SARS CoV2
2 days ago by Adyasha • 0
0
votes
5
replies
328
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 6 days ago by ▴ 20 • written 10 days ago by • 0
1
vote
2
replies
241
views
Downloading full alignments from Pfam
pfam
4 days ago by bef1 • 0
2
votes
2
replies
352
views
absolute path for symbolic links in Snakefile
Snakemake
updated 28 minutes ago by ▴ 50 • written 19 days ago by ▴ 60
0
votes
4
replies
379
views
Highest variable features in single cell data
single-cell
2 days ago by carolofharvest ▴ 40
5
votes
5
replies
619
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 5 days ago by • 0 • written 14 days ago by ★ 3.9k
1
vote
2
replies
413
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
15 hours ago by Zeng Hao ▴ 40
1
vote
6
replies
358
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 6 days ago by 142k • written 24 days ago by ▴ 80
1
vote
0
replies
170
views
phasing tumor long-reads
nanopore ONT haplotag phasing tumor
1 hour ago by eebloom ▴ 80
0
votes
2
replies
248
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
1 day ago by sainavyav22 • 0
1
vote
2
replies
287
views
read length in structural variant calling
nanopore SV QC ONT variant
6 days ago by eebloom ▴ 80
0
votes
0
replies
179
views
CellPhoneDB results
cellphonedb cpdb cell_surface_proteins
updated 2 days ago by 142k • written 10 weeks ago by ▴ 20
1
vote
10
replies
857
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 3 days ago by • 0 • written 3 months ago by ▴ 30
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 3 hours ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
15
replies
1.6k
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 5 days ago by ★ 7.1k • written 4 months ago by ▴ 10
2
votes
4
replies
710
views
Count all variants from vcf file
variants vcf Count
updated 2 days ago by 161k • written 20 months ago by • 0
0
votes
3
replies
672
views
Pluritest for pluripotency broken
pluripotent pluritest cells stem
updated 8 hours ago by • 0 • written 21 months ago by • 0
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 6 days ago by • 0 • written 12.8 years ago by ★ 1.7k
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 4 days ago by ▴ 10 • written 24 months ago by • 0
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 6 days ago by • 0 • written 2.2 years ago by • 0
0
votes
1
reply
547
views
HOMER on AWS
HOMER
updated 6 days ago by • 0 • written 2.2 years ago by ★ 1.4k
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 1 day ago by ▴ 10 • written 2.5 years ago by • 0
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 6 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 2 days ago by 161k • written 5.7 years ago by ▴ 180
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR statistical test parametric non-parametric
updated 5 days ago by ▴ 210 • written 3.8 years ago by ▴ 40
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
4 days ago by Ibrahim Tanyalcin ★ 1.2k
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 6 days ago by 142k • written 4.5 years ago by ▴ 20
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 1 day ago by • 0 • written 5.1 years ago by ★ 1.8k
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 3 days ago by • 0 • written 6.1 years ago by ▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 3 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 5 days ago by • 0 • written 10.2 years ago by ▴ 20
197 results • Page 4 of 4
Recent Votes
Comment: WGCNA gene selection: gene significance or LASSO?
WGCNA gene selection: gene significance or LASSO?
Comment: absolute path for symbolic links in Snakefile
Answer: absolute path for symbolic links in Snakefile
A: Remove sequences <300 bases from FASTA file
Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
A: Insert Size And Fragment Size ?
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Recent Awards • All
Scholar to tim.booth ▴ 50
Popular Question to strive • 0
Popular Question to LauferVA 4.2k
Popular Question to ManuelDB ▴ 80
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Scholar to Pierre Lindenbaum 161k
Recent Replies
Answer: Snakemake fails to find conda in PBS by tim.booth ▴ 50
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile by tim.booth ▴ 50
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length by Pierre Lindenbaum 161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file by sainavyav22 • 0
Here you go. 1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput 2.perl annotate_variation.pl 100…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant. Your question is ambiguous because you…
Comment: Help with Biopython for Beginner by GenoMax 142k
> That turns it into a mess of paragraphs See above. Select (highlight with mouse) the part you want to represent as `code` and then click…
Comment: Help with Biopython for Beginner by cput • 0
That turns it into a mess of paragraphs, but if it truly is more productive thanks for the tip!
Comment: Presence of unknown sites in ANNOVAR output file by Ram 43k
Please show us your full annovar command line.
Comment: input file for alternative splicing in rmats in linux by Ram 43k
I've done what I can to make your post more professional. Stick to outlining your problem, personal pleas do not really belong on a profess…
Comment: Contig assembly task, errors by rackbersingh • 0
Hi Phillip, Thanks for providing an answer and clearing up some confusion, looking into what you said about older assemblers reverse comp…
Comment: How to analyze Infinium Mouse Methylation BeadChip array data? by Tawny ▴ 180
Did you get this figured out? I am having the same error in R.
Answer: JASPAR2024_getMatrixSet error by Raghad • 0
Try this: ```r #Read the motifs library(JASPAR2024) library(TFBSTools) jaspar <- JASPAR2024() sq24 <- RSQLite::dbConnect(RSQLite::SQLite…
Answer: How to convert normalized BigWig file to count matrix? by ATpoint 82k
It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned to…
Comment: bcftools - reducing to "sites-only"? by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: bcftools - reducing to "sites-only"? by Matthew • 0
Thank you Pierre! Not sure why I didn't notice that (I should have)
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