Showing : ShortRead • reset
4
votes
7
replies
2.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
15 months ago Bernardo ▴ 10
0
votes
3
replies
1.3k
views
ShortRead Installation in R 4.2.0 and zlib library
R-4 ShortRead
18 months ago Bogdan ▴ 670
1
vote
1
reply
873
views
Unable to install "scruff" with BiocManager::install()
scruff Install ShortRead
updated 20 months ago by 3.9k • written 20 months ago by • 0
1
vote
3
replies
857
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
2.0 years ago kent.riemondy ▴ 20
0
votes
4
replies
1.1k
views
BiocParallel: bplapply invents data
BiocParallel ShortRead
3.1 years ago robmaz77 ▴ 20
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
3.2 years ago robmaz77 ▴ 20
2
votes
3
replies
1.7k
views
Running old packages on Mac
ShortRead
written 3.2 years ago by ▴ 90
0
votes
3
replies
1.3k
views
ShortRead: how to convert qualities?
ShortRead FastqQuality
3.2 years ago robmaz77 ▴ 20
0
votes
2
replies
1.6k
views
Cannot Install ShortRead Package
ShortRead
written 3.4 years ago by • 0
0
votes
7
replies
2.3k
views
Cannot install ShortRead package
ShortRead
updated 3.4 years ago by 25k • written 3.5 years ago by • 0
0
votes
3
replies
1.3k
views
ShortRead Error message: invalid character '
shortread fastq
4.6 years ago lauren.fitch • 0
14
votes
21
replies
11k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation shortread dependency
updated 4.9 years ago by ▴ 240 • written 6.0 years ago by ▴ 60
12
votes
7
replies
1.9k
views
No method for coercing this S4 class to a vector, as trying to import my own data rather than using SRA in the workflow RnaSeqGeneEdgeRQL
rnaseqgeneedgerql shortread Rsubread
updated 5.1 years ago by ▴ 60 • written 5.1 years ago by ▴ 60
0
votes
2
replies
1.7k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 5.3 years ago by 0 • written 15.3 years ago by ★ 1.9k
1
vote
1
reply
1.0k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 10
1
vote
3
replies
1.4k
views
Remove reads from raw fastq
shortread biostrings
updated 5.5 years ago by 50k • written 5.5 years ago by • 0
0
votes
4
replies
3.7k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.6 years ago ferbecneu • 0
0
votes
4
replies
957
views
Should I use legacy functions in ShortRead package?
shortread
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 20
4
votes
3
replies
1.5k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread pacbio fastq
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 50
4
votes
5
replies
1.7k
views
No BAM option in readAligned from the ShortRead package
bioconductor shortread bam file nucler
updated 6.2 years ago by ★ 1.5k • written 6.2 years ago by ▴ 10
1
vote
2
replies
1.3k
views
bplapply with ShortRead functions
shortread biocparallel
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 100
1
vote
2
replies
1.5k
views
Reading fastq file after narrowing sequences
ShortRead FastqStreamer
6.4 years ago ioannis.vardaxis ▴ 30
0
votes
2
replies
1.5k
views
readFastq error reading Nanopore fastq
shortread
6.7 years ago kamal.fartiyal84 ▴ 10
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 7.1 years ago by 16k • written 7.1 years ago by ▴ 70
3
votes
10
replies
4.5k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 20
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.7 years ago David ▴ 860
1
vote
2
replies
1.4k
views
Shortread convert S4 vector qualityScore to vector
shortread
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 90
0
votes
1
reply
1.2k
views
make: *** [ShortRead.so] Error 1
shortread
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Error Raised When Trying To Use pileup()
hilbertvis rsamtools shortread biostrings
updated 7.9 years ago by 25k • written 7.9 years ago by • 0
5
votes
1
reply
3.3k
views
Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
8.1 years ago phil.chapman ▴ 150
1
vote
2
replies
1.7k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 150
5
votes
7
replies
2.3k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Error with qa() in package ShortRead when checking for adapter contamination.
shortread
8.2 years ago Diego Diez ▴ 760
0
votes
1
reply
1.2k
views
ShortRead::FastqStreamer() causes segfault
shortread segfault
8.4 years ago Watal M. Iwasaki ▴ 10
4
votes
7
replies
2.2k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 20
1
vote
1
reply
2.4k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 10
0
votes
2
replies
1.5k
views
ShortRead Error in slot(object, ".srlist")
software error ShortRead
updated 8.6 years ago by 25k • written 8.6 years ago by • 0
1
vote
2
replies
1.6k
views
Why I'm getting an error when using ShortRead package's FastqStreamerList function?
shortread fastqSteamerList
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 10
1
vote
2
replies
2.2k
views
FastqSampler with trimmed paired-end reads
shortread
updated 3.2 years ago by ▴ 20 • written 8.8 years ago by ▴ 20
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago danova_fr ▴ 20
0
votes
4
replies
1.6k
views
gcContent error with shortread
shortread
9.0 years ago danova_fr ▴ 20
2
votes
5
replies
1.9k
views
ShortRead trim sequence at specific position
shortread fastq
9.1 years ago • updated 9.0 years ago danova_fr ▴ 20
5
votes
4
replies
3.3k
views
Trimming with ShortRead
shortread
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 20
0
votes
2
replies
1.3k
views
ShortRead summary stats
shortread illumina
9.1 years ago danova_fr ▴ 20
1
vote
7
replies
5.9k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
5
votes
1
reply
3.2k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 100
0
votes
3
replies
2.7k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by • 0
0
votes
3
replies
1.7k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread readAligned reverseComplement ScanBamParam
9.3 years ago jdavison ▴ 10
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.6 years ago patrick.schordert ▴ 30
0
votes
0
replies
988
views
Longest continuous sequence from multiple alignment
GO ShortRead GO ShortRead
10.0 years ago Guest User ★ 13k
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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