Showing : shortread • reset
1
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10
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ShortRead with large fastq files
shortread
10.6 years ago danova_fr ▴ 20
14
votes
21
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13k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation shortread dependency
updated 6.6 years ago by ▴ 240 • written 7.7 years ago by ▴ 60
5
votes
5
replies
2.7k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
11.4 years ago patrick.schordert ▴ 30
0
votes
5
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2.4k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 16.4 years ago by 25k • written 16.4 years ago by ▴ 40
1
vote
7
replies
6.9k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 10.8 years ago by 25k • written 10.8 years ago by • 0
12
votes
7
replies
3.6k
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 6.8 years ago by ▴ 60 • written 6.8 years ago by ▴ 60
0
votes
11
replies
3.3k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
14.2 years ago Stefanie Ververs ▴ 70
2
votes
5
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2.5k
views
ShortRead trim sequence at specific position
shortread fastq
10.8 years ago • updated 10.7 years ago danova_fr ▴ 20
0
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2
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2.2k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 7.0 years ago by 0 • written 17.0 years ago by ★ 1.9k
0
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5
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1.9k
views
Error Raised When Trying To Use pileup()
hilbertvis rsamtools shortread biostrings
updated 9.7 years ago by 25k • written 9.7 years ago by • 0
1
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2
replies
1.7k
views
FastqStreamer and qualitytype
shortread
9.4 years ago David ▴ 860
0
votes
3
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2.2k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread readAligned reverseComplement ScanBamParam
11.0 years ago jdavison ▴ 10
4
votes
5
replies
2.5k
views
No BAM option in readAligned from the ShortRead package
bioconductor shortread bam file nucler
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by ▴ 10
0
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2
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1.7k
views
mismatch & replacement
ShortRead ShortRead
updated 15.2 years ago by ▴ 590 • written 15.2 years ago by ▴ 90
0
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4
replies
1.9k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
15.3 years ago heyi xiao ▴ 360
0
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2
replies
1.7k
views
ShortRead summary stats
shortread illumina
10.8 years ago danova_fr ▴ 20
0
votes
4
replies
5.7k
views
Retrieving specific sequences from a fastq
shortread biostrings
7.3 years ago ferbecneu • 0
0
votes
2
replies
2.0k
views
readFastq error reading Nanopore fastq
shortread
8.4 years ago kamal.fartiyal84 ▴ 10
0
votes
4
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2.1k
views
gcContent error with shortread
shortread
10.7 years ago danova_fr ▴ 20
0
votes
3
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3.2k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 13.1 years ago by 25k • written 13.1 years ago by ▴ 310
0
votes
3
replies
1.7k
views
ShortRead QA
Sequencing ShortRead Sequencing ShortRead
updated 15.5 years ago by 25k • written 15.5 years ago by ▴ 650
0
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2
replies
1.4k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 16.3 years ago by 25k • written 16.3 years ago by ▴ 40
0
votes
1
reply
847
views
report a possible bug of
ShortRead ShortRead
updated 13.9 years ago by 25k • written 13.9 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead ShortRead
updated 13.7 years ago by 25k • written 13.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
ShortRead package
ShortRead ShortRead
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 260
0
votes
1
reply
1.1k
views
how to plot quality report
ShortRead ShortRead
updated 13.4 years ago by 25k • written 13.4 years ago by ★ 2.0k
0
votes
1
reply
1.4k
views
trimTails function in ShortRead package give different results on the same input
Sequencing ShortRead Sequencing ShortRead
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 10
0
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4
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1.3k
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 13.2 years ago by 25k • written 13.2 years ago by ★ 2.0k
0
votes
3
replies
7.5k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 310
0
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3
replies
3.3k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 410
0
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3
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2.7k
views
bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 12.8 years ago by ★ 8.2k • written 12.8 years ago by ▴ 680
0
votes
5
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2.2k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 12.4 years ago by ★ 6.8k • written 12.4 years ago by ▴ 300
0
votes
2
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3.6k
views
ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
PROcess ShortRead PROcess ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 300
0
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3
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3.5k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by • 0
5
votes
1
reply
3.8k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 10.9 years ago by 25k • written 10.9 years ago by ▴ 100
5
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4
replies
4.3k
views
Trimming with ShortRead
shortread
updated 10.8 years ago by 25k • written 10.8 years ago by ▴ 20
1
vote
2
replies
3.0k
views
FastqSampler with trimmed paired-end reads
shortread
updated 4.9 years ago by ▴ 20 • written 10.6 years ago by ▴ 20
1
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2
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2.0k
views
Why I'm getting an error when using ShortRead package's FastqStreamerList function?
shortread fastqSteamerList
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 10
1
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1
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1.4k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 10
0
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1
reply
1.3k
views
A question about ShortRead_1.8.2.tar.gz.
ShortRead ShortRead
updated 15.0 years ago by 25k • written 15.0 years ago by ★ 8.2k
0
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2
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1.5k
views
FastqSampler sort by ID
ShortRead ShortRead
updated 13.2 years ago by 25k • written 13.2 years ago by ▴ 390
0
votes
1
reply
1.0k
views
Vignette for ShortRead
ShortRead ShortRead
updated 17.5 years ago by 25k • written 17.5 years ago by ▴ 330
0
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1
reply
1.2k
views
Problems reading multiple MAQ map files with ShortRead ReadAligned
Cancer PROcess ShortRead charm Cancer PROcess ShortRead charm
16.9 years ago Martin Morgan 25k
0
votes
1
reply
1.0k
views
possible bug in extendReads() in package chipseq
Alignment ShortRead Alignment ShortRead
updated 16.2 years ago by 25k • written 16.2 years ago by ▴ 40
0
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2
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1.2k
views
ShortRead internal: too many 'snap' entries
ShortRead ShortRead
updated 16.1 years ago by 25k • written 16.1 years ago by ▴ 160
0
votes
1
reply
1.2k
views
Shortread and filtering of duplicate reads
ShortRead ShortRead
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 50
0
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2
replies
1.4k
views
ShortRead with BAM
ShortRead ShortRead
updated 15.7 years ago by 68k • written 15.7 years ago by ▴ 210
0
votes
1
reply
1.0k
views
Typo in ?FastqQuality help page?
ShortRead ShortRead
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 950
0
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1
reply
1.3k
views
ShortRead information
ShortRead ShortRead
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 10
0
votes
3
replies
2.5k
views
Error installing Rsamtools
ShortRead Rsamtools ShortRead Rsamtools
updated 15.7 years ago by 25k • written 15.7 years ago by ★ 1.3k
96 results • Page 1 of 2
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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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