Showing : shortread • reset
1
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10
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3.9k
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ShortRead with large fastq files
shortread
9.9 years ago danova_fr ▴ 20
14
votes
21
replies
12k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation shortread dependency
updated 5.9 years ago by ▴ 240 • written 7.0 years ago by ▴ 60
5
votes
5
replies
2.4k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
10.6 years ago patrick.schordert ▴ 30
0
votes
5
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2.2k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 40
1
vote
7
replies
6.5k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 10.1 years ago by 25k • written 10.1 years ago by • 0
12
votes
7
replies
3.0k
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 6.1 years ago by ▴ 60 • written 6.1 years ago by ▴ 60
0
votes
11
replies
2.8k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
13.5 years ago Stefanie Ververs ▴ 70
2
votes
5
replies
2.2k
views
ShortRead trim sequence at specific position
shortread fastq
10.1 years ago • updated 10.0 years ago danova_fr ▴ 20
0
votes
2
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2.0k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 6.3 years ago by 0 • written 16.3 years ago by ★ 1.9k
0
votes
5
replies
1.7k
views
Error Raised When Trying To Use pileup()
hilbertvis rsamtools shortread biostrings
updated 8.9 years ago by 25k • written 8.9 years ago by • 0
1
vote
2
replies
1.5k
views
FastqStreamer and qualitytype
shortread
8.7 years ago David ▴ 860
0
votes
3
replies
2.0k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread readAligned reverseComplement ScanBamParam
10.3 years ago jdavison ▴ 10
4
votes
5
replies
2.2k
views
No BAM option in readAligned from the ShortRead package
bioconductor shortread bam file nucler
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 10
0
votes
2
replies
1.5k
views
mismatch & replacement
ShortRead ShortRead
updated 14.5 years ago by ▴ 590 • written 14.5 years ago by ▴ 90
0
votes
4
replies
1.7k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
14.6 years ago heyi xiao ▴ 360
0
votes
2
replies
1.5k
views
ShortRead summary stats
shortread illumina
10.1 years ago danova_fr ▴ 20
0
votes
4
replies
5.1k
views
Retrieving specific sequences from a fastq
shortread biostrings
6.6 years ago ferbecneu • 0
0
votes
2
replies
1.8k
views
readFastq error reading Nanopore fastq
shortread
7.7 years ago kamal.fartiyal84 ▴ 10
0
votes
4
replies
1.9k
views
gcContent error with shortread
shortread
10.0 years ago danova_fr ▴ 20
0
votes
3
replies
2.9k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 310
0
votes
3
replies
1.5k
views
ShortRead QA
Sequencing ShortRead Sequencing ShortRead
updated 14.8 years ago by 25k • written 14.8 years ago by ▴ 650
0
votes
2
replies
1.3k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 15.6 years ago by 25k • written 15.6 years ago by ▴ 40
0
votes
1
reply
772
views
report a possible bug of
ShortRead ShortRead
updated 13.2 years ago by 25k • written 13.2 years ago by ★ 2.0k
0
votes
1
reply
932
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 10
0
votes
1
reply
969
views
ShortRead package
ShortRead ShortRead
updated 12.8 years ago by 25k • written 12.8 years ago by ▴ 260
0
votes
1
reply
982
views
how to plot quality report
ShortRead ShortRead
updated 12.7 years ago by 25k • written 12.7 years ago by ★ 2.0k
0
votes
1
reply
1.3k
views
trimTails function in ShortRead package give different results on the same input
Sequencing ShortRead Sequencing ShortRead
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 10
0
votes
4
replies
1.2k
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 12.5 years ago by 25k • written 12.5 years ago by ★ 2.0k
0
votes
3
replies
7.1k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 310
0
votes
3
replies
3.0k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 410
0
votes
3
replies
2.5k
views
bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 12.1 years ago by ★ 8.2k • written 12.1 years ago by ▴ 680
0
votes
5
replies
1.9k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 11.7 years ago by ★ 6.8k • written 11.7 years ago by ▴ 300
0
votes
2
replies
3.4k
views
ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
PROcess ShortRead PROcess ShortRead
updated 11.4 years ago by 25k • written 11.4 years ago by ▴ 300
0
votes
3
replies
3.2k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by • 0
5
votes
1
reply
3.5k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 100
5
votes
4
replies
3.9k
views
Trimming with ShortRead
shortread
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 20
1
vote
2
replies
2.7k
views
FastqSampler with trimmed paired-end reads
shortread
updated 4.2 years ago by ▴ 20 • written 9.8 years ago by ▴ 20
1
vote
2
replies
1.9k
views
Why I'm getting an error when using ShortRead package's FastqStreamerList function?
shortread fastqSteamerList
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 10
1
vote
1
reply
1.3k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 6.4 years ago by 25k • written 6.4 years ago by ▴ 10
0
votes
1
reply
1.2k
views
A question about ShortRead_1.8.2.tar.gz.
ShortRead ShortRead
updated 14.3 years ago by 25k • written 14.3 years ago by ★ 8.2k
0
votes
2
replies
1.4k
views
FastqSampler sort by ID
ShortRead ShortRead
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 390
0
votes
1
reply
869
views
Vignette for ShortRead
ShortRead ShortRead
updated 16.8 years ago by 25k • written 16.8 years ago by ▴ 330
0
votes
1
reply
1.1k
views
Problems reading multiple MAQ map files with ShortRead ReadAligned
Cancer PROcess ShortRead charm Cancer PROcess ShortRead charm
16.1 years ago Martin Morgan 25k
0
votes
1
reply
937
views
possible bug in extendReads() in package chipseq
Alignment ShortRead Alignment ShortRead
updated 15.4 years ago by 25k • written 15.4 years ago by ▴ 40
0
votes
2
replies
1.1k
views
ShortRead internal: too many 'snap' entries
ShortRead ShortRead
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 160
0
votes
1
reply
1.1k
views
Shortread and filtering of duplicate reads
ShortRead ShortRead
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 50
0
votes
2
replies
1.2k
views
ShortRead with BAM
ShortRead ShortRead
updated 15.0 years ago by 68k • written 15.0 years ago by ▴ 210
0
votes
1
reply
875
views
Typo in ?FastqQuality help page?
ShortRead ShortRead
updated 14.9 years ago by 25k • written 14.9 years ago by ▴ 950
0
votes
1
reply
1.2k
views
ShortRead information
ShortRead ShortRead
updated 14.9 years ago by 25k • written 14.9 years ago by ▴ 10
0
votes
3
replies
2.3k
views
Error installing Rsamtools
ShortRead Rsamtools ShortRead Rsamtools
updated 14.9 years ago by 25k • written 14.9 years ago by ★ 1.3k
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Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
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> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
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Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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