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 • updated 14 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
861
views
Unable to install "scruff" with BiocManager::install()
scruff Install ShortRead
updated 20 months ago by 3.8k • written 20 months ago by • 0
1
vote
3
replies
843
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
1.6k
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 3.4 years ago by • 0
0
votes
3
replies
1.3k
views
ShortRead Error message: invalid character '
shortread fastq
4.5 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
951
views
Should I use legacy functions in ShortRead package?
shortread
updated 6.1 years ago by 25k • written 6.1 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
1.2k
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
1.4k
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 7.0 years ago by 16k • written 7.0 years ago by ▴ 70
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 7.4 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
8.0 years ago phil.chapman ▴ 150
1
vote
2
replies
1.7k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 8.0 years ago by 25k • written 8.0 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
1.2k
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
2.1k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
1
vote
1
reply
2.4k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 8.4 years ago by 25k • written 8.4 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
1.8k
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
3.2k
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
977
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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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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