Showing : fastq • reset
0
votes
1
reply
1.3k
views
Seqinr for FASTQ files?
fastq fast seqinr
updated 2.9 years ago by ★ 4.7k • written 2.9 years ago by • 0
7
votes
12
replies
5.6k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 2.8 years ago by 52k • written 9.3 years ago by • 0
0
votes
3
replies
3.9k
views
How to count barcode sequences in a fastq file
fastq barcoding
updated 3.5 years ago by ★ 4.0k • written 3.6 years ago by ▴ 30
2
votes
3
replies
2.8k
views
error when reading fastq file
FastqCleaner fastq ShortRead
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
3
votes
9
replies
10k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 4.2 years ago by • 0 • written 9.6 years ago by • 0
0
votes
3
replies
1.6k
views
ShortRead Error message: invalid character '
shortread fastq
5.4 years ago lauren.fitch • 0
2
votes
3
replies
1.9k
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 5.7 years ago by ★ 3.6k • written 5.7 years ago by ▴ 60
7
votes
4
replies
4.0k
views
Convert BAM to FASTQ
BAM FASTQ
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 30
7
votes
7
replies
6.2k
views
What are the methods to get count data per cell from single cell fastq given only R1, R2, and I1 fastq files
fastq single cell
updated 6.0 years ago by 52k • written 6.0 years ago by ▴ 380
0
votes
2
replies
6.1k
views
Converting Fastq to Fasta in R
R Bioinformatics Fastq Fasta
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
0
votes
0
replies
1.1k
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
6.3 years ago A ▴ 40
0
votes
0
replies
1.2k
views
Sequencing database tool in R: tracking Sanger and NGS of large-scale directed evolution projects
rmysql fastq seqinr ngs sangerseqr
6.8 years ago JoeMG • 0
4
votes
3
replies
1.8k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread pacbio fastq
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 50
3
votes
10
replies
5.5k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 20
0
votes
2
replies
1.5k
views
How to start CrispRVariants with fastq file starting point
R crispr fastq
8.3 years ago kfburbach • 0
2
votes
1
reply
1.6k
views
Uniting SRA Data into a single file
R fastq SRA sradb
updated 8.3 years ago by 25k • written 8.3 years ago by • 0
0
votes
2
replies
3.1k
views
subset from fastq file
fastq
8.5 years ago KB ▴ 50
0
votes
1
reply
2.3k
views
Error downloading using SRAdb
fastq sradb ftp
updated 9.0 years ago by ▴ 170 • written 9.0 years ago by • 0
1
vote
9
replies
3.5k
views
need help manipulating fastq file
fastq
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 50
0
votes
2
replies
3.4k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 9.8 years ago by 68k • written 9.8 years ago by • 0
2
votes
5
replies
2.1k
views
ShortRead trim sequence at specific position
shortread fastq
9.9 years ago • updated 9.8 years ago danova_fr ▴ 20
5
votes
1
reply
3.5k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 100
22 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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