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193 results • Page 1 of 4
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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
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 1 day ago by 161k • written 5.7 years ago by ▴ 180
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 4 days ago by ★ 7.1k • written 4 months ago by ▴ 10
13
votes
14
replies
794
views
High Malat-1 expression in single cell data
single-cell
updated 19 hours ago by ▴ 40 • written 9 days ago by ▴ 40
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
10
votes
14
replies
644
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 1 day ago by 142k • written 7 days 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 5 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 2 days ago by • 0 • written 6.1 years ago by ▴ 20
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 18 hours ago by • 0 • written 4.8 years ago by ▴ 60
1
vote
10
replies
853
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 2 days ago by • 0 • written 3 months ago by ▴ 30
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 5 days ago by • 0 • written 2.2 years ago by • 0
0
votes
9
replies
1.4k
views
kinannote software installation problems
kinannote
updated 6 hours ago by • 0 • written 5.7 years ago by ▴ 30
3
votes
8
replies
518
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
2 days ago by Qroid ▴ 40
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
1
vote
7
replies
467
views
Question regarding WGCNA
WGCNA Network-construction
updated 6 hours ago by 43k • written 5 days ago by • 0
1
vote
7
replies
453
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
5 days ago by eebloom ▴ 80
1
vote
7
replies
521
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
0
votes
7
replies
417
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 9 hours ago by ★ 2.0k • written 2 days ago by ▴ 140
0
votes
7
replies
569
views
Post-imputation plot
michigan-imputation-server quality-control
updated 6 days ago by 3.9k • written 9 days ago by ▴ 10
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 3 days ago by ▴ 10 • written 24 months ago by • 0
1
vote
6
replies
358
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 5 days ago by 142k • written 23 days ago by ▴ 80
0
votes
6
replies
425
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 5 days ago by 14k • written 5 days ago by • 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 2 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
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 14 hours ago by ▴ 10 • written 2.5 years ago by • 0
0
votes
6
replies
312
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
updated 5 days ago by ★ 6.0k • written 6 days ago by • 0
1
vote
6
replies
676
views
anRichment is missing
WGCNA anRichment
updated 2 days ago by 142k • written 5 months ago by ▴ 180
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 11 hours ago by • 0 • written 5.1 years ago by ★ 1.8k
1
vote
5
replies
199
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 1 day ago by 19k • written 1 day ago by ★ 1.8k
0
votes
5
replies
189
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 14 hours ago by 21k • written 17 hours ago by • 0
0
votes
5
replies
326
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 5 days ago by ▴ 20 • written 9 days ago by • 0
0
votes
5
replies
237
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
11 hours ago by me • 0
4
votes
5
replies
3.3k
views
How to compare compare two Sam files to check mapping
alignment
updated 10 hours ago by ▴ 90 • written 6.4 years ago by ▴ 60
5
votes
5
replies
612
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 13 days ago by ★ 3.9k
3
votes
5
replies
286
views
Generating mpileup file using samtools
mpileup samtools
updated 5 days ago by 21k • written 5 days ago by • 0
0
votes
5
replies
350
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 5 days ago by 10k • written 5 days ago by ▴ 750
1
vote
5
replies
306
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
updated 17 hours ago by 54k • written 1 day ago by • 0
5
votes
5
replies
284
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 6 days ago by ▴ 30 • written 6 days ago by ▴ 150
1
vote
5
replies
378
views
HCL database download
HCL
updated 1 day ago by 43k • written 4 days ago by ▴ 20
1
vote
5
replies
296
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 2 days ago by 43k • written 2 days ago by • 0
1
vote
5
replies
342
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
5 days ago by Riccardo ▴ 10
3
votes
5
replies
332
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
5 days ago by Maverick ▴ 10
0
votes
5
replies
366
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 5 days ago by ▴ 180 • written 6 days ago by • 0
1
vote
5
replies
368
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 2 days ago by 43k • written 3 days ago by • 0
5
votes
5
replies
253
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
23 hours ago by Chris ▴ 280
2
votes
4
replies
710
views
Count all variants from vcf file
variants vcf Count
updated 1 day ago by 161k • written 20 months ago by • 0
0
votes
4
replies
376
views
Highest variable features in single cell data
single-cell
1 day ago by carolofharvest ▴ 40
1
vote
4
replies
331
views
Understanding STAR output (Aligned.out.sam file)
STAR paired-end read
1 day ago by heelpPlease • 0
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 14 hours ago by • 0 • written 5.5 years ago by 8.4k
3
votes
4
replies
412
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 2 days ago by ★ 7.1k • written 5 days ago by ▴ 40
5
votes
4
replies
388
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
6 days ago by Estevão • 0
193 results • Page 1 of 4
Recent Votes
Answer: How can I analyze normalized expression data?
Answer: How can I analyze normalized expression data?
Answer: Pruning Phylogenetic Trees and Bootstrap Values
Difference between Pysam Pileup and Fetch
Answer: Where can I download some example BAM files?
Comment: Where can I download some example BAM files?
Where can I download some example BAM files?
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Recent Replies
Comment: How can I analyze normalized expression data? by mnx0723 • 0
thank you for comment
Comment: Pruning Phylogenetic Trees and Bootstrap Values by Zeng Hao ▴ 40
Dear Klaus, Thank you for the reply. If I could clarify with an example: With this tree, B0----------------- A -| B1----------…
Answer: Contig assembly task, errors by Philipp Bayer 8.4k
Feels a bit strange for an aptitude test, feels more like homework. 1) seems OK to me, just chuck them into CAP3 and see what falls out.…
Comment: Help with Biopython for Beginner by Pierre Lindenbaum 161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: bcftools - reducing to "sites-only"? by Pierre Lindenbaum 161k
bcftools view -G in.vcf.gz <!-- Diabetic foot ulceration (DFU) is a devastating complication of diabetes whose pathogenesis rema…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
I probably got some of the vocabulary wrong. I thought that "Dom HOR2932 HOR3036 HOR3726 KWSBambina Rec S42IL_124" were representing my ge…
Comment: featureCounts output assigned value higher than and HISAT2 mapping. by Ram 43k
It's featureCount**s**, not featureCount. I've edited your post and fixed all mentions of featureCounts.
Comment: kinannote software installation problems by Emanoelle • 0
Hey, I know it's been 5 years but I have the same issue. When I run the test the software is unable to perform and always deliver the follo…
Comment: STAR aligner error by Ram 43k
If they can't help you, we probably can't do much either. But we can optimize your STAR command. BAM SortedByCoordinate is the worst settin…
Answer: Obtaining Infinium Methylation450K manifest for hg38 by marco.barr ▴ 90
Hi, you can check it from github here: [https://zwdzwd.github.io/InfiniumAnnotation][1]. I don't know if this is what you are looking fo…
Comment: RNA seq analysis by ATpoint 82k
It makes absolutely no sense to conduct such an analysis. I strongly discourage you to even start with it. Results will be utterly nonsense…
Comment: Differentail gene expression results by swbarnes2 14k
Cross-posted: https://support.bioconductor.org/p/9158194/
Answer: Seurat V5 integration by Bastien Hervé 5.3k
It will depend on your context and question. I guess you will want to compare gene expression between your conditions within cell types …
Answer: Error in plotting PCA plot in seurat by Adam ▴ 30
You get this error when you try to compare two data frames that have different dimensions. Try using the traceback() command to figure out …
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
Sorry, this was supposed to be a comment appended to the chain above. I didn't mean to post as an answer.
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