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 5.0 years ago by ▴ 240 • written 6.1 years ago by ▴ 60
0
votes
11
replies
2.3k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
12.6 years ago Stefanie Ververs ▴ 70
3
votes
10
replies
4.6k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 7.5 years ago by 66k • written 7.5 years ago by ▴ 20
1
vote
10
replies
3.1k
views
ShortRead with large fastq files
shortread
9.0 years ago danova_fr ▴ 20
0
votes
7
replies
2.4k
views
Cannot install ShortRead package
ShortRead
updated 3.5 years ago by 25k • written 3.5 years ago by • 0
12
votes
7
replies
2.0k
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 5.1 years ago by ▴ 60 • written 5.2 years ago by ▴ 60
5
votes
7
replies
2.4k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 20
4
votes
7
replies
2.1k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
16 months ago • updated 15 months ago Bernardo ▴ 10
4
votes
7
replies
2.2k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 20
1
vote
7
replies
6.0k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 9.2 years ago by 25k • written 9.2 years ago by • 0
2
votes
6
replies
1.3k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
3.3 years ago robmaz77 ▴ 20
0
votes
5
replies
1.5k
views
ShortRead error when reading BAM file
ShortRead ShortRead
updated 12.7 years ago by 25k • written 12.7 years ago by ▴ 650
2
votes
5
replies
1.9k
views
ShortRead trim sequence at specific position
shortread fastq
9.1 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
9.7 years ago patrick.schordert ▴ 30
0
votes
5
replies
1.3k
views
Error Raised When Trying To Use pileup()
hilbertvis rsamtools shortread biostrings
updated 8.0 years ago by 25k • written 8.0 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 6.3 years ago by ★ 1.5k • written 6.3 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 14.7 years ago by 25k • written 14.8 years ago by ▴ 40
0
votes
5
replies
1.6k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 10.8 years ago by ★ 6.8k • written 10.8 years ago by ▴ 300
0
votes
4
replies
1.6k
views
gcContent error with shortread
shortread
9.1 years ago danova_fr ▴ 20
5
votes
4
replies
3.3k
views
Trimming with ShortRead
shortread
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 20
0
votes
4
replies
1.2k
views
fastq upload time
ShortRead ShortRead
updated 13.7 years ago by 21k • written 13.7 years ago by ▴ 90
0
votes
4
replies
1.4k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
13.7 years ago heyi xiao ▴ 360
0
votes
4
replies
1.1k
views
BiocParallel: bplapply invents data
BiocParallel ShortRead
3.2 years ago robmaz77 ▴ 20
0
votes
4
replies
3.8k
views
Retrieving specific sequences from a fastq
shortread biostrings
5.7 years ago ferbecneu • 0
0
votes
4
replies
980
views
Should I use legacy functions in ShortRead package?
shortread
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 20
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 7.1 years ago by 16k • written 7.1 years ago by ▴ 70
0
votes
4
replies
969
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 11.6 years ago by 25k • written 11.6 years ago by ★ 2.0k
0
votes
3
replies
2.1k
views
Error installing Rsamtools
ShortRead Rsamtools ShortRead Rsamtools
updated 14.0 years ago by 25k • written 14.0 years ago by ★ 1.3k
0
votes
3
replies
2.5k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 310
0
votes
3
replies
1.3k
views
ShortRead Error message: invalid character '
shortread fastq
4.6 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 6.3 years ago by 25k • written 6.3 years ago by ▴ 50
0
votes
3
replies
1.3k
views
ShortRead: how to convert qualities?
ShortRead FastqQuality
3.3 years ago robmaz77 ▴ 20
1
vote
3
replies
878
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
2.1 years ago kent.riemondy ▴ 20
0
votes
3
replies
6.1k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 11.3 years ago by 25k • written 11.3 years ago by ▴ 310
2
votes
3
replies
1.7k
views
Running old packages on Mac
ShortRead
written 3.3 years ago by ▴ 90
0
votes
3
replies
2.8k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 9.4 years ago by ★ 6.8k • written 9.4 years ago by • 0
0
votes
3
replies
1.7k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread readAligned reverseComplement ScanBamParam
9.4 years ago jdavison ▴ 10
0
votes
3
replies
1.4k
views
ShortRead Installation in R 4.2.0 and zlib library
R-4 ShortRead
19 months ago Bogdan ▴ 670
0
votes
3
replies
1.3k
views
Problem installing Rsamtools and ShortRead under Fedora 10.
ShortRead Rsamtools ShortRead Rsamtools
updated 13.6 years ago by 6.7k • written 13.6 years ago by ▴ 50
0
votes
3
replies
2.7k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 11.3 years ago by 25k • written 11.3 years ago by ▴ 410
1
vote
3
replies
1.5k
views
Remove reads from raw fastq
shortread biostrings
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
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
3
replies
1.3k
views
ShortRead QA
Sequencing ShortRead Sequencing ShortRead
updated 13.9 years ago by 25k • written 13.9 years ago by ▴ 650
1
vote
2
replies
1.3k
views
FastqStreamer and qualitytype
shortread
7.7 years ago David ▴ 860
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
2
replies
1.7k
views
Solexa fastq files and BLAT
Cancer Biostrings ShortRead Cancer Biostrings ShortRead
updated 5.4 years ago by 0 • written 15.4 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
927
views
ShortRead internal: too many 'snap' entries
ShortRead ShortRead
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 160
0
votes
2
replies
997
views
ShortRead with BAM
ShortRead ShortRead
updated 14.1 years ago by 66k • written 14.1 years ago by ▴ 210
0
votes
2
replies
1.2k
views
mismatch & replacement
ShortRead ShortRead
updated 13.6 years ago by ▴ 590 • written 13.6 years ago by ▴ 90
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Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
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If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
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Reduce the number of nodes appear in the cnetplot of clusterprofiler
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