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
11
replies
2.3k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
12.5 years ago • updated 12.4 years ago Stefanie Ververs ▴ 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 7.3 years ago by 65k • written 7.3 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
7
replies
2.2k
views
Cannot install ShortRead package
ShortRead
updated 3.4 years ago by 25k • written 3.4 years ago by • 0
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
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
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
14 months ago Bernardo ▴ 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
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
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
3.2 years ago robmaz77 ▴ 20
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
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread fastq
9.0 years ago danova_fr ▴ 20
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
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
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
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
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
4
replies
1.6k
views
gcContent error with shortread
shortread
9.0 years ago • updated 8.9 years ago danova_fr ▴ 20
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
0
votes
4
replies
1.1k
views
fastq upload time
ShortRead ShortRead
updated 13.6 years ago by 21k • written 13.6 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
4
replies
1.1k
views
BiocParallel: bplapply invents data
BiocParallel ShortRead
3.1 years ago robmaz77 ▴ 20
0
votes
4
replies
3.6k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.5 years ago ferbecneu • 0
0
votes
4
replies
939
views
Should I use legacy functions in ShortRead package?
shortread
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 20
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
4
replies
945
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 11.4 years ago by 25k • written 11.4 years ago by ★ 2.0k
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
0
votes
3
replies
2.5k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 11.3 years ago by 25k • written 11.3 years ago by ▴ 310
0
votes
3
replies
1.3k
views
ShortRead Error message: invalid character '
shortread fastq
4.5 years ago lauren.fitch • 0
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
3
replies
1.3k
views
ShortRead: how to convert qualities?
ShortRead FastqQuality
3.2 years ago robmaz77 ▴ 20
1
vote
3
replies
827
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
24 months ago kent.riemondy ▴ 20
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
2
votes
3
replies
1.6k
views
Running old packages on Mac
ShortRead
written 3.2 years ago by ▴ 90
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
0
votes
3
replies
1.2k
views
ShortRead Installation in R 4.2.0 and zlib library
R-4 ShortRead
18 months ago Bogdan ▴ 670
0
votes
3
replies
1.3k
views
Problem installing Rsamtools and ShortRead under Fedora 10.
ShortRead Rsamtools ShortRead Rsamtools
updated 13.5 years ago by 6.7k • written 13.5 years ago by ▴ 50
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
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
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
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
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.6 years ago David ▴ 860
0
votes
2
replies
1.2k
views
FastqSampler sort by ID
ShortRead ShortRead
updated 11.4 years ago by 25k • written 11.4 years ago by ▴ 390
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
0
votes
2
replies
1.1k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 14.5 years ago by 25k • written 14.5 years ago by ▴ 40
0
votes
2
replies
906
views
ShortRead internal: too many 'snap' entries
ShortRead ShortRead
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 160
0
votes
2
replies
977
views
ShortRead with BAM
ShortRead ShortRead
updated 14.0 years ago by 65k • written 14.0 years ago by ▴ 210
0
votes
2
replies
1.2k
views
mismatch & replacement
ShortRead ShortRead
updated 13.5 years ago by ▴ 590 • written 13.5 years ago by ▴ 90
50 results • Page 1 of 1
Recent ...
Replies
Comment: geneList error in clusterprofiler by Ana • 0
Ahh thank you, that fixed it!
Answer: geneList error in clusterprofiler by Basti ▴ 750
Have a look at the documentation : https://www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4/topics/gseGO geneList argument s…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks again for your answer, I will try to play a little bit with the parameters. Only one thing, my data are actually CpG methylation :)…
Comment: flowStats Search Error by tholmes • 0
Thank you so much!
Comment: what is the sampleFiles by James W. MacDonald 65k
I don't see any sampleFiles argument for any function in that package. Ideally you would at least tell us what function you are using.
Votes
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
United States, just now
France, 4 minutes ago
Brazil, 4 minutes ago
Wageningen University, Wageningen, the Netherlands, 7 minutes ago
Switzerland, 12 minutes ago
Traffic: 921 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6