Showing : shortread • reset
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
2.0k
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
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
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
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.7 years ago patrick.schordert ▴ 30
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
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
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
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
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
7
replies
2.1k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
15 months ago Bernardo ▴ 10
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
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
2
votes
3
replies
1.7k
views
Running old packages on Mac
ShortRead
written 3.2 years ago by ▴ 90
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
2
votes
6
replies
1.3k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
3.2 years ago robmaz77 ▴ 20
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
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
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.7 years ago David ▴ 860
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
9.0 years ago danova_fr ▴ 20
1
vote
2
replies
1.5k
views
Reading fastq file after narrowing sequences
ShortRead FastqStreamer
6.5 years ago ioannis.vardaxis ▴ 30
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
2.3k
views
FastqSampler with trimmed paired-end reads
shortread
updated 3.2 years ago by ▴ 20 • written 8.9 years ago by ▴ 20
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
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
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
7
replies
6.0k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 9.2 years ago by 25k • written 9.2 years ago by • 0
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
1
vote
3
replies
862
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
2.1 years ago kent.riemondy ▴ 20
1
vote
1
reply
883
views
Unable to install "scruff" with BiocManager::install()
scruff Install ShortRead
updated 20 months ago by 3.9k • written 20 months ago by • 0
0
votes
1
reply
1.0k
views
remove empty short read after using trimEnds
ShortRead ShortRead
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 40
0
votes
2
replies
1.7k
views
Rsamtools installation error
ShortRead Rsamtools ShortRead Rsamtools
updated 12.3 years ago by 25k • written 12.3 years ago by ▴ 60
0
votes
1
reply
651
views
report a possible bug of
ShortRead ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ★ 2.0k
0
votes
0
replies
703
views
report a possible bug of
Cancer ShortRead Cancer ShortRead
12.2 years ago Martin Morgan 25k
0
votes
1
reply
776
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead ShortRead
updated 12.0 years ago by 25k • written 12.0 years ago by ▴ 10
0
votes
1
reply
836
views
ShortRead package
ShortRead ShortRead
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 260
0
votes
1
reply
833
views
how to plot quality report
ShortRead ShortRead
updated 11.8 years ago by 25k • written 11.8 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
trimTails function in ShortRead package give different results on the same input
Sequencing ShortRead Sequencing ShortRead
updated 11.6 years ago by 25k • written 11.6 years ago by ▴ 10
0
votes
4
replies
958
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 11.5 years ago by 25k • written 11.5 years ago by ★ 2.0k
0
votes
0
replies
816
views
readAligned with bowtie2 input
Alignment ShortRead Alignment ShortRead
11.5 years ago Maria Dermit ▴ 10
0
votes
3
replies
2.5k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 11.4 years ago by 25k • written 11.4 years ago by ▴ 310
0
votes
3
replies
6.1k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 310
0
votes
3
replies
2.6k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 410
0
votes
0
replies
1.1k
views
Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
11.2 years ago Noah Dowell ▴ 410
0
votes
3
replies
2.2k
views
bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 11.1 years ago by ★ 8.2k • written 11.1 years ago by ▴ 680
0
votes
5
replies
1.6k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 10.7 years ago by ★ 6.8k • written 10.7 years ago by ▴ 300
0
votes
2
replies
3.2k
views
ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
PROcess ShortRead PROcess ShortRead
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 300
0
votes
0
replies
990
views
Longest continuous sequence from multiple alignment
GO ShortRead GO ShortRead
10.0 years ago Guest User ★ 13k
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
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
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Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue by shepherl 3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis by Guido Hooiveld ★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
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A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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