Showing : ShortRead • reset
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago danova_fr ▴ 20
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
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
1.9k
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
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
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
0
votes
11
replies
2.3k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
12.5 years ago Stefanie Ververs ▴ 70
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread fastq
9.0 years ago danova_fr ▴ 20
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
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
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.6 years ago David ▴ 860
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
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
2
replies
1.2k
views
mismatch & replacement
ShortRead ShortRead
updated 13.5 years ago by ▴ 590 • written 13.5 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
2
replies
1.3k
views
ShortRead summary stats
shortread illumina
9.1 years ago danova_fr ▴ 20
0
votes
4
replies
3.6k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.5 years ago ferbecneu • 0
0
votes
2
replies
1.4k
views
readFastq error reading Nanopore fastq
shortread
6.6 years ago kamal.fartiyal84 ▴ 10
0
votes
4
replies
1.6k
views
gcContent error with shortread
shortread
9.0 years ago danova_fr ▴ 20
0
votes
3
replies
2.5k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 11.4 years ago by 25k • written 11.4 years ago by ▴ 310
0
votes
3
replies
1.3k
views
ShortRead QA
Sequencing ShortRead Sequencing ShortRead
updated 13.7 years ago by 25k • written 13.8 years ago by ▴ 650
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
1
reply
639
views
report a possible bug of
ShortRead ShortRead
updated 12.1 years ago by 25k • written 12.1 years ago by ★ 2.0k
0
votes
1
reply
765
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead ShortRead
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 10
0
votes
1
reply
824
views
ShortRead package
ShortRead ShortRead
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 260
0
votes
1
reply
823
views
how to plot quality report
ShortRead ShortRead
updated 11.7 years ago by 25k • written 11.7 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
trimTails function in ShortRead package give different results on the same input
Sequencing ShortRead Sequencing ShortRead
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 10
0
votes
4
replies
948
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
6.0k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 310
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
2.2k
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
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
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
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
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
5
votes
4
replies
3.2k
views
Trimming with ShortRead
shortread
updated 9.0 years ago by 25k • written 9.1 years ago by ▴ 20
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
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
1
reply
1.0k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.0k
views
A question about ShortRead_1.8.2.tar.gz.
ShortRead ShortRead
updated 13.3 years ago by 25k • written 13.3 years ago by ★ 8.2k
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
1
reply
725
views
Vignette for ShortRead
ShortRead ShortRead
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 330
0
votes
1
reply
873
views
Problems reading multiple MAQ map files with ShortRead ReadAligned
Cancer PROcess ShortRead charm Cancer PROcess ShortRead charm
15.1 years ago Martin Morgan 25k
0
votes
1
reply
789
views
possible bug in extendReads() in package chipseq
Alignment ShortRead Alignment ShortRead
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 40
0
votes
2
replies
907
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
1
reply
900
views
Shortread and filtering of duplicate reads
ShortRead ShortRead
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 50
0
votes
2
replies
979
views
ShortRead with BAM
ShortRead ShortRead
updated 14.0 years ago by 65k • written 14.0 years ago by ▴ 210
0
votes
1
reply
725
views
Typo in ?FastqQuality help page?
ShortRead ShortRead
updated 13.9 years ago by 25k • written 13.9 years ago by ▴ 940
0
votes
1
reply
998
views
ShortRead information
ShortRead ShortRead
updated 13.9 years ago by 25k • written 13.9 years ago by ▴ 10
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) has nothing to do with normalization. It isn't clear why not subsetting would cause any difficu…
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Awards • All
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Popular Question to W. Evan Johnson ▴ 850
Popular Question to Alejandro Reyes ★ 1.9k
Locations • All
WEHI, Melbourne, Australia, just now
France, 1 minute ago
Switzerland, 5 minutes ago
Germany, 13 minutes ago
Germany, 15 minutes ago
Traffic: 866 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