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fastq
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724
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Seqinr for FASTQ files?
fastq
fast
seqinr
updated 18 months ago by
ATpoint
★ 3.4k • written 18 months ago by
hank00000
• 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
Gordon Smyth
48k • written 7.9 years ago by
hamidrezarazzaghian
• 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
Kevin Blighe
3.8k • written 2.1 years ago by
yura.grabovska
▴ 30
2
votes
3
replies
1.7k
views
error when reading fastq file
FastqCleaner
fastq
ShortRead
updated 2.6 years ago by
James W. MacDonald
63k • written 2.6 years ago by
sinanoori88
• 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
Rafael
• 0 • written 8.2 years ago by
mk.applebee
• 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
Wei Shi
★ 3.5k • written 4.3 years ago by
Raito92
▴ 60
7
votes
4
replies
2.7k
views
Convert BAM to FASTQ
BAM
FASTQ
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
ioannis.vardaxis
▴ 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
Gordon Smyth
48k • written 4.6 years ago by
Matthew Thornton
▴ 350
0
votes
2
replies
4.4k
views
Converting Fastq to Fasta in R
R
Bioinformatics
Fastq
Fasta
updated 4.7 years ago by
James W. MacDonald
63k • written 4.7 years ago by
christinafragel
• 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
Martin Morgan
25k • written 5.6 years ago by
benjamin.j.callahan
▴ 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
James W. MacDonald
63k • written 6.8 years ago by
Frocha
▴ 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
Martin Morgan
25k • written 6.9 years ago by
grecoandreauni
• 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
Jack Zhu
▴ 170 • written 7.5 years ago by
yugi1001
• 0
1
vote
9
replies
2.4k
views
need help manipulating fastq file
fastq
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
KB
▴ 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
James W. MacDonald
63k • written 8.4 years ago by
greg.mulhearn
• 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
Martin Morgan
25k • written 8.6 years ago by
francesca.defilippis
▴ 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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