Showing : ShortRead • reset
4
votes
7
replies
1.3k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
10 months ago • updated 9 months ago Bernardo ▴ 10
0
votes
3
replies
909
views
ShortRead Installation in R 4.2.0 and zlib library
R-4 ShortRead
13 months ago Bogdan ▴ 670
1
vote
1
reply
626
views
Unable to install "scruff" with BiocManager::install()
scruff Install ShortRead
updated 15 months ago by 3.6k • written 15 months ago by • 0
1
vote
3
replies
695
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
19 months ago kent.riemondy • 0
0
votes
4
replies
906
views
BiocParallel: bplapply invents data
BiocParallel ShortRead
2.7 years ago robmaz77 ▴ 20
2
votes
6
replies
1.1k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
2.8 years ago robmaz77 ▴ 20
2
votes
3
replies
1.4k
views
Running old packages on Mac
ShortRead
written 2.8 years ago by ▴ 90
0
votes
3
replies
1.1k
views
ShortRead: how to convert qualities?
ShortRead FastqQuality
2.8 years ago robmaz77 ▴ 20
0
votes
2
replies
1.3k
views
Cannot Install ShortRead Package
ShortRead
written 3.0 years ago by • 0
0
votes
7
replies
1.9k
views
Cannot install ShortRead package
ShortRead
updated 3.0 years ago by 25k • written 3.0 years ago by • 0
0
votes
3
replies
1.1k
views
ShortRead Error message: invalid character '
shortread fastq
4.1 years ago lauren.fitch • 0
14
votes
21
replies
10k
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Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation shortread dependency
updated 4.5 years ago by ▴ 240 • written 5.6 years ago by ▴ 60
12
votes
7
replies
1.5k
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 4.7 years ago by ▴ 60 • written 4.7 years ago by ▴ 60
0
votes
2
replies
1.6k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 4.9 years ago by 0 • written 14.9 years ago by ★ 1.9k
1
vote
1
reply
912
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 5.0 years ago by 25k • written 5.0 years ago by ▴ 10
1
vote
3
replies
1.2k
views
Remove reads from raw fastq
shortread biostrings
updated 5.1 years ago by 48k • written 5.1 years ago by • 0
0
votes
4
replies
3.2k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.2 years ago ferbecneu • 0
0
votes
4
replies
844
views
Should I use legacy functions in ShortRead package?
shortread
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 10
4
votes
3
replies
1.3k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread pacbio fastq
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 50
4
votes
5
replies
1.5k
views
No BAM option in readAligned from the ShortRead package
bioconductor shortread bam file nucler
updated 5.8 years ago by ★ 1.5k • written 5.8 years ago by ▴ 10
1
vote
2
replies
1.1k
views
bplapply with ShortRead functions
shortread biocparallel
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 100
1
vote
2
replies
1.3k
views
Reading fastq file after narrowing sequences
ShortRead FastqStreamer
6.0 years ago ioannis.vardaxis ▴ 30
0
votes
2
replies
1.3k
views
readFastq error reading Nanopore fastq
shortread
6.3 years ago kamal.fartiyal84 ▴ 10
5
votes
4
replies
2.4k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 70
0
votes
10
replies
3.9k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 7.0 years ago by 64k • written 7.0 years ago by ▴ 10
1
vote
2
replies
1.1k
views
FastqStreamer and qualitytype
shortread
7.3 years ago David ▴ 860
1
vote
2
replies
1.3k
views
Shortread convert S4 vector qualityScore to vector
shortread
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 90
0
votes
1
reply
1.1k
views
make: *** [ShortRead.so] Error 1
shortread
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 10
0
votes
5
replies
1.2k
views
Error Raised When Trying To Use pileup()
hilbertvis rsamtools shortread biostrings
updated 7.5 years ago by 25k • written 7.5 years ago by • 0
5
votes
1
reply
3.1k
views
Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
7.6 years ago phil.chapman ▴ 150
1
vote
2
replies
1.6k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 150
5
votes
7
replies
2.1k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 20
0
votes
0
replies
1.2k
views
Error with qa() in package ShortRead when checking for adapter contamination.
shortread
7.8 years ago Diego Diez ▴ 760
0
votes
1
reply
1.1k
views
ShortRead::FastqStreamer() causes segfault
shortread segfault
8.0 years ago Watal M. Iwasaki ▴ 10
4
votes
7
replies
1.9k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 20
1
vote
1
reply
2.3k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 10
0
votes
2
replies
1.3k
views
ShortRead Error in slot(object, ".srlist")
software error ShortRead
updated 8.2 years ago by 25k • written 8.2 years ago by • 0
1
vote
2
replies
1.5k
views
Why I'm getting an error when using ShortRead package's FastqStreamerList function?
shortread fastqSteamerList
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 10
1
vote
2
replies
2.1k
views
FastqSampler with trimmed paired-end reads
shortread
updated 2.8 years ago by ▴ 20 • written 8.4 years ago by ▴ 20
1
vote
10
replies
2.7k
views
ShortRead with large fastq files
shortread
8.5 years ago danova_fr ▴ 20
0
votes
4
replies
1.4k
views
gcContent error with shortread
shortread
8.6 years ago danova_fr ▴ 20
2
votes
5
replies
1.7k
views
ShortRead trim sequence at specific position
shortread fastq
8.7 years ago • updated 8.6 years ago danova_fr ▴ 20
5
votes
4
replies
3.0k
views
Trimming with ShortRead
shortread
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 20
0
votes
2
replies
1.2k
views
ShortRead summary stats
shortread illumina
8.7 years ago danova_fr ▴ 20
1
vote
7
replies
5.7k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 8.7 years ago by 25k • written 8.7 years ago by • 0
5
votes
1
reply
2.9k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 100
0
votes
3
replies
2.5k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by • 0
0
votes
3
replies
1.5k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread readAligned reverseComplement ScanBamParam
8.9 years ago jdavison ▴ 10
5
votes
5
replies
1.9k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.2 years ago patrick.schordert ▴ 30
0
votes
0
replies
888
views
Longest continuous sequence from multiple alignment
GO ShortRead GO ShortRead
9.6 years ago Guest User ★ 12k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Tim Peters ▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by R_Page • 0
Thank you, this works well. As for CDNA, I figured out what I need to find, and have made a new post regarding it.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hello Michael, I am continuing here and need your expert answer on this again I have performed small rna loci and DNA methylation mappin…
Comment: GOslim missing GO term by amanda • 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Comment: GOslim missing GO term by James W. MacDonald 64k
Is this a WGCNA analysis (multiple co-expression clusters sounds like WGCNA)? If so, none of that is inferential or easily interpreted. It …
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Why is DMRcate not available for Bioconductor version 3.18?
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
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Scholar to James W. MacDonald 64k
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Popular Question to Gordon Smyth 48k
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