Showing : fastq • reset
0
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1
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1.5k
views
Seqinr for FASTQ files?
fastq fast seqinr
updated 3.7 years ago by ★ 5.0k • written 3.7 years ago by • 0
7
votes
12
replies
6.3k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 3.6 years ago by 53k • written 10.1 years ago by • 0
0
votes
3
replies
4.4k
views
How to count barcode sequences in a fastq file
fastq barcoding
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 30
2
votes
3
replies
3.2k
views
error when reading fastq file
FastqCleaner fastq ShortRead
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
3
votes
9
replies
11k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 5.0 years ago by • 0 • written 10.4 years ago by • 0
0
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3
replies
1.8k
views
ShortRead Error message: invalid character '
shortread fastq
6.2 years ago lauren.fitch • 0
2
votes
3
replies
2.2k
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 6.5 years ago by ★ 3.6k • written 6.5 years ago by ▴ 60
7
votes
4
replies
4.5k
views
Convert BAM to FASTQ
BAM FASTQ
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 30
7
votes
7
replies
7.0k
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 6.7 years ago by 53k • written 6.8 years ago by ▴ 390
0
votes
2
replies
6.6k
views
Converting Fastq to Fasta in R
R Bioinformatics Fastq Fasta
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
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0
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1.2k
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
7.1 years ago A ▴ 60
0
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0
replies
1.4k
views
Sequencing database tool in R: tracking Sanger and NGS of large-scale directed evolution projects
rmysql fastq seqinr ngs sangerseqr
7.6 years ago JoeMG • 0
4
votes
3
replies
2.1k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread pacbio fastq
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 50
3
votes
10
replies
6.2k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 9.0 years ago by 68k • written 9.0 years ago by ▴ 20
0
votes
2
replies
1.8k
views
How to start CrispRVariants with fastq file starting point
R crispr fastq
9.0 years ago kfburbach • 0
2
votes
1
reply
1.8k
views
Uniting SRA Data into a single file
R fastq SRA sradb
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
0
votes
2
replies
3.5k
views
subset from fastq file
fastq
9.3 years ago KB ▴ 50
0
votes
1
reply
2.5k
views
Error downloading using SRAdb
fastq sradb ftp
updated 9.7 years ago by ▴ 170 • written 9.7 years ago by • 0
1
vote
9
replies
4.0k
views
need help manipulating fastq file
fastq
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 50
0
votes
2
replies
3.7k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 10.6 years ago by 68k • written 10.6 years ago by • 0
2
votes
5
replies
2.4k
views
ShortRead trim sequence at specific position
shortread fastq
10.7 years ago • updated 10.6 years ago danova_fr ▴ 20
5
votes
1
reply
3.7k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 10.8 years ago by 25k • written 10.8 years ago by ▴ 100
22 results • Page 1 of 1
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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