Showing : shortread • reset
14
votes
21
replies
12k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation shortread dependency
updated 5.9 years ago by ▴ 240 • written 7.0 years ago by ▴ 60
12
votes
7
replies
3.0k
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 6.1 years ago by ▴ 60 • written 6.1 years ago by ▴ 60
5
votes
1
reply
3.5k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 100
5
votes
1
reply
3.7k
views
Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
9.0 years ago phil.chapman ▴ 150
5
votes
5
replies
2.4k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
10.6 years ago patrick.schordert ▴ 30
5
votes
4
replies
3.9k
views
Trimming with ShortRead
shortread
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 20
5
votes
7
replies
2.9k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 20
5
votes
4
replies
3.2k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 70
4
votes
7
replies
2.6k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 20
4
votes
3
replies
1.9k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread pacbio fastq
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 50
4
votes
8
replies
3.9k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
updated 9 months ago by • 0 • written 2.3 years ago by ▴ 10
4
votes
5
replies
2.2k
views
No BAM option in readAligned from the ShortRead package
bioconductor shortread bam file nucler
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 10
3
votes
10
replies
5.7k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 20
2
votes
3
replies
2.1k
views
Running old packages on Mac
ShortRead
written 4.2 years ago by ▴ 90
2
votes
5
replies
2.2k
views
ShortRead trim sequence at specific position
shortread fastq
10.1 years ago • updated 10.0 years ago danova_fr ▴ 20
2
votes
6
replies
1.6k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
4.2 years ago robmaz77 ▴ 20
1
vote
2
replies
1.9k
views
Why I'm getting an error when using ShortRead package's FastqStreamerList function?
shortread fastqSteamerList
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 10
1
vote
2
replies
1.7k
views
Shortread convert S4 vector qualityScore to vector
shortread
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 90
1
vote
2
replies
1.5k
views
FastqStreamer and qualitytype
shortread
8.7 years ago David ▴ 860
1
vote
10
replies
3.9k
views
ShortRead with large fastq files
shortread
9.9 years ago danova_fr ▴ 20
1
vote
2
replies
1.9k
views
Reading fastq file after narrowing sequences
ShortRead FastqStreamer
7.4 years ago ioannis.vardaxis ▴ 30
1
vote
2
replies
1.6k
views
bplapply with ShortRead functions
shortread biocparallel
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 100
1
vote
2
replies
2.7k
views
FastqSampler with trimmed paired-end reads
shortread
updated 4.2 years ago by ▴ 20 • written 9.8 years ago by ▴ 20
1
vote
2
replies
2.0k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 150
1
vote
3
replies
2.0k
views
Remove reads from raw fastq
shortread biostrings
updated 6.5 years ago by 52k • written 6.5 years ago by • 0
1
vote
1
reply
1.3k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 6.4 years ago by 25k • written 6.4 years ago by ▴ 10
1
vote
7
replies
6.5k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 10.1 years ago by 25k • written 10.1 years ago by • 0
1
vote
1
reply
2.7k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 9.4 years ago by 25k • written 9.5 years ago by ▴ 10
1
vote
3
replies
1.2k
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
3.0 years ago kent.riemondy ▴ 20
1
vote
1
reply
1.2k
views
Unable to install "scruff" with BiocManager::install()
scruff Install ShortRead
updated 2.7 years ago by 4.1k • written 2.7 years ago by • 0
0
votes
1
reply
1.2k
views
remove empty short read after using trimEnds
ShortRead ShortRead
updated 13.4 years ago by 25k • written 13.4 years ago by ▴ 40
0
votes
2
replies
2.0k
views
Rsamtools installation error
ShortRead Rsamtools ShortRead Rsamtools
updated 13.2 years ago by 25k • written 13.2 years ago by ▴ 60
0
votes
1
reply
772
views
report a possible bug of
ShortRead ShortRead
updated 13.2 years ago by 25k • written 13.2 years ago by ★ 2.0k
0
votes
0
replies
809
views
report a possible bug of
Cancer ShortRead Cancer ShortRead
13.2 years ago Martin Morgan 25k
0
votes
1
reply
932
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 10
0
votes
1
reply
969
views
ShortRead package
ShortRead ShortRead
updated 12.8 years ago by 25k • written 12.8 years ago by ▴ 260
0
votes
1
reply
982
views
how to plot quality report
ShortRead ShortRead
updated 12.7 years ago by 25k • written 12.7 years ago by ★ 2.0k
0
votes
1
reply
1.3k
views
trimTails function in ShortRead package give different results on the same input
Sequencing ShortRead Sequencing ShortRead
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 10
0
votes
4
replies
1.2k
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 12.5 years ago by 25k • written 12.5 years ago by ★ 2.0k
0
votes
0
replies
949
views
readAligned with bowtie2 input
Alignment ShortRead Alignment ShortRead
12.4 years ago Maria Dermit ▴ 10
0
votes
3
replies
2.9k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 310
0
votes
3
replies
7.1k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 310
0
votes
3
replies
3.0k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 410
0
votes
0
replies
1.3k
views
Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
12.2 years ago Noah Dowell ▴ 410
0
votes
3
replies
2.5k
views
bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 12.1 years ago by ★ 8.2k • written 12.1 years ago by ▴ 680
0
votes
5
replies
1.9k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 11.7 years ago by ★ 6.8k • written 11.7 years ago by ▴ 300
0
votes
2
replies
3.4k
views
ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
PROcess ShortRead PROcess ShortRead
updated 11.4 years ago by 25k • written 11.4 years ago by ▴ 300
0
votes
0
replies
1.2k
views
Longest continuous sequence from multiple alignment
GO ShortRead GO ShortRead
11.0 years ago Guest User ★ 13k
0
votes
3
replies
2.0k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread readAligned reverseComplement ScanBamParam
10.3 years ago jdavison ▴ 10
0
votes
3
replies
3.2k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Module membership vs gene significance result and Modules-trait relationships re by Vinaya • 0
Hi. I am having the same issue, and haven't found a solution still.
Comment: Feature Counts - potential bug with outfile.jcounts by Tom • 0
[Penistone Locksmith][1] I think that would be a great idea; a novel junction to annotated junction proximity output column. So if the nove…
Comment: Filtering after DESeq by caroline.zanchi • 0
I am going to try this right now, thanks !
Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Votes
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
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