Showing : fastq • reset
0
votes
1
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724
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Seqinr for FASTQ files?
fastq fast seqinr
updated 18 months ago by ★ 3.4k • written 18 months ago by • 0
7
votes
12
replies
4.1k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 16 months ago by 48k • written 7.9 years ago by • 0
0
votes
3
replies
2.6k
views
How to count barcode sequences in a fastq file
fastq barcoding
updated 2.1 years ago by 3.8k • written 2.1 years ago by ▴ 30
2
votes
3
replies
1.7k
views
error when reading fastq file
FastqCleaner fastq ShortRead
updated 2.6 years ago by 63k • written 2.6 years ago by • 0
3
votes
9
replies
8.1k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 2.8 years ago by • 0 • written 8.2 years ago by • 0
0
votes
3
replies
1.0k
views
ShortRead Error message: invalid character '
shortread fastq
4.0 years ago lauren.fitch • 0
2
votes
3
replies
1.2k
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 4.3 years ago by ★ 3.5k • written 4.3 years ago by ▴ 60
7
votes
4
replies
2.7k
views
Convert BAM to FASTQ
BAM FASTQ
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 30
7
votes
7
replies
4.5k
views
What are the methods to get count data per cell from single cell fastq given only R1, R2, and I1 fastq files
fastq single cell
updated 4.6 years ago by 48k • written 4.6 years ago by ▴ 350
0
votes
2
replies
4.4k
views
Converting Fastq to Fasta in R
R Bioinformatics Fastq Fasta
updated 4.7 years ago by 63k • written 4.7 years ago by • 0
0
votes
0
replies
700
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
4.9 years ago A ▴ 40
0
votes
0
replies
799
views
Sequencing database tool in R: tracking Sanger and NGS of large-scale directed evolution projects
rmysql fastq seqinr ngs sangerseqr
5.4 years ago JoeMG • 0
4
votes
3
replies
1.2k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread pacbio fastq
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 50
0
votes
10
replies
3.7k
views
How to check that the reads in two fastq files are in the same order
shortread fastq
updated 6.8 years ago by 63k • written 6.8 years ago by ▴ 10
0
votes
2
replies
1.1k
views
How to start CrispRVariants with fastq file starting point
R crispr fastq
6.8 years ago kfburbach • 0
2
votes
1
reply
1.1k
views
Uniting SRA Data into a single file
R fastq SRA sradb
updated 6.9 years ago by 25k • written 6.9 years ago by • 0
0
votes
2
replies
2.5k
views
subset from fastq file
fastq
7.1 years ago KB ▴ 50
0
votes
1
reply
1.7k
views
Error downloading using SRAdb
fastq sradb ftp
updated 7.5 years ago by ▴ 170 • written 7.5 years ago by • 0
1
vote
9
replies
2.4k
views
need help manipulating fastq file
fastq
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 50
0
votes
2
replies
2.8k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2 deseqdataset rnaseqgene fastq reference genome
updated 8.4 years ago by 63k • written 8.4 years ago by • 0
2
votes
5
replies
1.6k
views
ShortRead trim sequence at specific position
shortread fastq
8.5 years ago • updated 8.4 years ago danova_fr ▴ 20
5
votes
1
reply
2.8k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 100
22 results • Page 1 of 1
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Replies
Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles) by Dorien ▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by andrew.b.kleist • 0
This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…
Votes
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
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