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 5.9 years ago by ▴ 60
0
votes
3
replies
6.0k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 310
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
3
votes
10
replies
4.4k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 7.3 years ago by 65k • written 7.3 years ago by ▴ 20
0
votes
4
replies
3.6k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.5 years ago ferbecneu • 0
5
votes
1
reply
3.2k
views
Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
8.0 years ago phil.chapman ▴ 150
5
votes
4
replies
3.2k
views
Trimming with ShortRead
shortread
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 20
5
votes
1
reply
3.1k
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
2
replies
3.1k
views
ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
PROcess ShortRead PROcess ShortRead
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 300
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago danova_fr ▴ 20
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
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 70
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
3
replies
2.5k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 11.3 years ago by 25k • written 11.4 years ago by ▴ 310
1
vote
1
reply
2.4k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
5
votes
7
replies
2.3k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 20
0
votes
11
replies
2.3k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
12.5 years ago Stefanie Ververs ▴ 70
0
votes
7
replies
2.2k
views
Cannot install ShortRead package
ShortRead
updated 3.4 years ago by 25k • written 3.4 years ago by • 0
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
0
votes
3
replies
2.2k
views
bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 11.0 years ago by ★ 8.2k • written 11.0 years ago by ▴ 680
4
votes
7
replies
2.1k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
0
votes
3
replies
2.0k
views
Error installing Rsamtools
ShortRead Rsamtools ShortRead Rsamtools
updated 13.9 years ago by 25k • written 13.9 years ago by ★ 1.3k
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
4
votes
7
replies
1.9k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
15 months ago • updated 14 months ago Bernardo ▴ 10
0
votes
5
replies
1.9k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 14.6 years ago by 25k • written 14.6 years ago by ▴ 40
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 5.0 years ago by ▴ 60 • written 5.0 years ago by ▴ 60
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread fastq
9.0 years ago danova_fr ▴ 20
1
vote
2
replies
1.7k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 150
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
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
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
2
replies
1.7k
views
Rsamtools installation error
ShortRead Rsamtools ShortRead Rsamtools
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 60
2
votes
3
replies
1.6k
views
Running old packages on Mac
ShortRead
written 3.2 years ago by ▴ 90
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
0
votes
2
replies
1.6k
views
Cannot Install ShortRead Package
ShortRead
written 3.4 years ago by • 0
0
votes
4
replies
1.6k
views
gcContent error with shortread
shortread
9.0 years ago danova_fr ▴ 20
0
votes
5
replies
1.5k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 10.6 years ago by ★ 6.8k • written 10.6 years ago by ▴ 300
0
votes
5
replies
1.5k
views
ShortRead error when reading BAM file
ShortRead ShortRead
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 650
1
vote
2
replies
1.5k
views
Reading fastq file after narrowing sequences
ShortRead FastqStreamer
6.4 years ago ioannis.vardaxis ▴ 30
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
0
votes
2
replies
1.5k
views
ShortRead Error in slot(object, ".srlist")
software error ShortRead
updated 8.5 years ago by 25k • written 8.5 years ago by • 0
0
votes
2
replies
1.4k
views
readFastq error reading Nanopore fastq
shortread
6.6 years ago kamal.fartiyal84 ▴ 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
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
4
replies
1.4k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
13.6 years ago heyi xiao ▴ 360
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
0
votes
2
replies
1.3k
views
ShortRead summary stats
shortread illumina
9.1 years ago danova_fr ▴ 20
0
votes
3
replies
1.3k
views
ShortRead QA
Sequencing ShortRead Sequencing ShortRead
updated 13.7 years ago by 25k • written 13.7 years ago by ▴ 650
0
votes
3
replies
1.3k
views
ShortRead: how to convert qualities?
ShortRead FastqQuality
3.2 years ago robmaz77 ▴ 20
0
votes
1
reply
1.3k
views
shortread readAligned with BWA
GO ShortRead GO ShortRead
updated 12.7 years ago by 25k • written 12.7 years ago by ▴ 280
50 results • Page 1 of 1
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Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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