Showing : ShortRead • reset
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 6.0 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
3
votes
10
replies
4.4k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 20
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago danova_fr ▴ 20
0
votes
7
replies
2.2k
views
Cannot install ShortRead package
ShortRead
updated 3.4 years ago by 25k • written 3.4 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 5.1 years ago by ▴ 60
5
votes
7
replies
2.3k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 20
4
votes
7
replies
2.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
15 months ago • updated 14 months ago Bernardo ▴ 10
4
votes
7
replies
2.1k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
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
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
3.2 years ago robmaz77 ▴ 20
0
votes
5
replies
1.5k
views
ShortRead error when reading BAM file
ShortRead ShortRead
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 650
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread fastq
9.0 years ago danova_fr ▴ 20
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
1.3k
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
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
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 14.7 years ago by ▴ 40
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
4
replies
1.6k
views
gcContent error with shortread
shortread
9.0 years ago danova_fr ▴ 20
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
0
votes
4
replies
1.2k
views
fastq upload time
ShortRead ShortRead
updated 13.6 years ago by 21k • written 13.6 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
4
replies
1.1k
views
BiocParallel: bplapply invents data
BiocParallel ShortRead
3.1 years ago robmaz77 ▴ 20
0
votes
4
replies
3.6k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.6 years ago ferbecneu • 0
0
votes
4
replies
943
views
Should I use legacy functions in ShortRead package?
shortread
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 20
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 70
0
votes
4
replies
949
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
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
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 Error message: invalid character '
shortread fastq
4.5 years ago lauren.fitch • 0
4
votes
3
replies
1.5k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread pacbio fastq
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 50
0
votes
3
replies
1.3k
views
ShortRead: how to convert qualities?
ShortRead FastqQuality
3.2 years ago robmaz77 ▴ 20
1
vote
3
replies
836
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
2.0 years ago kent.riemondy ▴ 20
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
2
votes
3
replies
1.6k
views
Running old packages on Mac
ShortRead
written 3.2 years ago by ▴ 90
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
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
0
votes
3
replies
1.3k
views
ShortRead Installation in R 4.2.0 and zlib library
R-4 ShortRead
18 months ago Bogdan ▴ 670
0
votes
3
replies
1.3k
views
Problem installing Rsamtools and ShortRead under Fedora 10.
ShortRead Rsamtools ShortRead Rsamtools
updated 13.5 years ago by 6.7k • written 13.5 years ago by ▴ 50
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
1
vote
3
replies
1.4k
views
Remove reads from raw fastq
shortread biostrings
updated 5.5 years ago by 50k • written 5.5 years ago by • 0
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
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
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.6 years ago David ▴ 860
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
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
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
2
replies
908
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
2
replies
981
views
ShortRead with BAM
ShortRead ShortRead
updated 14.0 years ago by 65k • written 14.0 years ago by ▴ 210
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: minfi::read.metharray.exp by Basti ▴ 780
This is indeed correct now !
Comment: get BM error by Fara • 0
Thank you for the reply. The examples are these. ENSGACG00000014473 ENSGACG00000015168 ENSGACG00000007529
Comment: get BM error by Mike Smith ★ 6.5k
Can you provide an example of the Ensemble IDs you're trying to convert?
Comment: How to retrieve gene ontology GO class? by bandconductor • 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Votes
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
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