Showing : shortread • reset
1
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10
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4.5k
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ShortRead with large fastq files
shortread
10.7 years ago danova_fr ▴ 20
14
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21
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13k
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Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation shortread dependency
updated 6.7 years ago by ▴ 240 • written 7.8 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 16.5 years ago by 25k • written 16.5 years ago by ▴ 40
1
vote
7
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7.0k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 10.9 years ago by 25k • written 10.9 years ago by • 0
12
votes
7
replies
3.7k
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 6.9 years ago by ▴ 60 • written 6.9 years ago by ▴ 60
0
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11
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3.3k
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NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
14.3 years ago Stefanie Ververs ▴ 70
2
votes
5
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2.5k
views
ShortRead trim sequence at specific position
shortread fastq
10.9 years ago • updated 10.8 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 7.1 years ago by 0 • written 17.1 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
9.5 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
11.1 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 8.0 years ago by ★ 1.6k • written 8.0 years ago by ▴ 10
0
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2
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1.7k
views
mismatch & replacement
ShortRead ShortRead
updated 15.3 years ago by ▴ 590 • written 15.3 years ago by ▴ 90
0
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4
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1.9k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
15.4 years ago heyi xiao ▴ 360
0
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2
replies
1.7k
views
ShortRead summary stats
shortread illumina
10.9 years ago danova_fr ▴ 20
0
votes
4
replies
5.8k
views
Retrieving specific sequences from a fastq
shortread biostrings
7.4 years ago ferbecneu • 0
0
votes
2
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2.0k
views
readFastq error reading Nanopore fastq
shortread
8.5 years ago kamal.fartiyal84 ▴ 10
0
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4
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2.1k
views
gcContent error with shortread
shortread
10.8 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 13.2 years ago by 25k • written 13.2 years ago by ▴ 310
0
votes
3
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1.7k
views
ShortRead QA
Sequencing ShortRead Sequencing ShortRead
updated 15.6 years ago by 25k • written 15.6 years ago by ▴ 650
0
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2
replies
1.4k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 16.4 years ago by 25k • written 16.4 years ago by ▴ 40
0
votes
1
reply
851
views
report a possible bug of
ShortRead ShortRead
updated 14.0 years ago by 25k • written 14.0 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 13.5 years ago by 25k • written 13.5 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
votes
4
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1.3k
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 13.3 years ago by 25k • written 13.3 years ago by ★ 2.0k
0
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3
replies
7.7k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 13.0 years ago by 25k • written 13.0 years ago by ▴ 310
0
votes
3
replies
3.3k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 13.0 years ago by 25k • written 13.0 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 12.9 years ago by ★ 8.2k • written 12.9 years ago by ▴ 680
0
votes
5
replies
2.2k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 12.5 years ago by ★ 6.8k • written 12.5 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 11.1 years ago by ★ 6.8k • written 11.1 years ago by • 0
5
votes
1
reply
3.8k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 100
5
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4
replies
4.3k
views
Trimming with ShortRead
shortread
updated 10.9 years ago by 25k • written 10.9 years ago by ▴ 20
1
vote
2
replies
3.1k
views
FastqSampler with trimmed paired-end reads
shortread
updated 5.0 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 10.5 years ago by 25k • written 10.5 years ago by ▴ 10
1
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1
reply
1.5k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 7.2 years ago by 25k • written 7.2 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 15.1 years ago by 25k • written 15.1 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 13.3 years ago by 25k • written 13.3 years ago by ▴ 390
0
votes
1
reply
1.0k
views
Vignette for ShortRead
ShortRead ShortRead
updated 17.6 years ago by 25k • written 17.6 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
1.1k
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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1.3k
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 16.1 years ago by 25k • written 16.1 years ago by ▴ 50
0
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2
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1.4k
views
ShortRead with BAM
ShortRead ShortRead
updated 15.8 years ago by 68k • written 15.8 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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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
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Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
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Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
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FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
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