Showing : shortread • reset
1
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10
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3.0k
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ShortRead with large fastq files
shortread
8.9 years ago danova_fr ▴ 20
14
votes
21
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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 6.0 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
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1.9k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 14.7 years ago by 25k • written 14.7 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 5.1 years ago by ▴ 60 • written 5.1 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
9.1 years ago • updated 9.0 years ago danova_fr ▴ 20
0
votes
2
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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
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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
7.7 years ago David ▴ 860
0
votes
3
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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
3.7k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.6 years ago ferbecneu • 0
0
votes
2
replies
1.4k
views
readFastq error reading Nanopore fastq
shortread
6.7 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 13.8 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 14.6 years ago by 25k • written 14.6 years ago by ▴ 40
0
votes
1
reply
644
views
report a possible bug of
ShortRead ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ★ 2.0k
0
votes
1
reply
767
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
829
views
ShortRead package
ShortRead ShortRead
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 260
0
votes
1
reply
829
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
951
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 11.5 years ago by 25k • written 11.5 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 11.1 years ago by ★ 8.2k • written 11.1 years ago by ▴ 680
0
votes
5
replies
1.5k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 10.7 years ago by ★ 6.8k • written 10.7 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
3.2k
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 9.1 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
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1
reply
1.0k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 5.4 years ago by 25k • written 5.4 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 11.5 years ago by 25k • written 11.5 years ago by ▴ 390
0
votes
1
reply
728
views
Vignette for ShortRead
ShortRead ShortRead
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 330
0
votes
1
reply
878
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
794
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
911
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
908
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
982
views
ShortRead with BAM
ShortRead ShortRead
updated 14.0 years ago by 65k • written 14.0 years ago by ▴ 210
0
votes
1
reply
732
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
1.0k
views
ShortRead information
ShortRead ShortRead
updated 13.9 years ago by 25k • written 13.9 years ago by ▴ 10
0
votes
3
replies
2.1k
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
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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