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fastq
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949
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Seqinr for FASTQ files?
fastq
fast
seqinr
updated 2.0 years ago by
ATpoint
★ 4.0k • written 2.0 years ago by
hank00000
• 0
7
votes
12
replies
4.7k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR
normalization
fastq
txt
TMM
updated 23 months ago by
Gordon Smyth
50k • written 8.4 years ago by
hamidrezarazzaghian
• 0
0
votes
3
replies
3.2k
views
How to count barcode sequences in a fastq file
fastq
barcoding
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
yura.grabovska
▴ 30
2
votes
3
replies
2.1k
views
error when reading fastq file
FastqCleaner
fastq
ShortRead
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
sinanoori88
• 0
3
votes
9
replies
8.9k
views
merge fastq.gz in R? (or in Windows?)
rnaseq
bioconductor
fastq
updated 3.4 years ago by
Rafael
• 0 • written 8.8 years ago by
mk.applebee
• 0
0
votes
3
replies
1.3k
views
ShortRead Error message: invalid character '
shortread
fastq
4.5 years ago
lauren.fitch
• 0
2
votes
3
replies
1.4k
views
Boxplot function not showing all reads length on x-axis
boxplot
reads
fastq
sequencing
rsubread
updated 4.9 years ago by
Wei Shi
★ 3.6k • written 4.9 years ago by
Raito92
▴ 60
7
votes
4
replies
3.2k
views
Convert BAM to FASTQ
BAM
FASTQ
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
ioannis.vardaxis
▴ 30
7
votes
7
replies
5.1k
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 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
Matthew Thornton
▴ 350
0
votes
2
replies
5.0k
views
Converting Fastq to Fasta in R
R
Bioinformatics
Fastq
Fasta
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
christinafragel
• 0
0
votes
0
replies
865
views
Quantifying reporter expression to validate sequencing
alignment
Fastq
fasta
5.4 years ago
A
▴ 40
0
votes
0
replies
951
views
Sequencing database tool in R: tracking Sanger and NGS of large-scale directed evolution projects
rmysql
fastq
seqinr
ngs
sangerseqr
6.0 years ago
JoeMG
• 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
Martin Morgan
25k • written 6.2 years ago by
benjamin.j.callahan
▴ 50
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 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
Frocha
▴ 20
0
votes
2
replies
1.3k
views
How to start CrispRVariants with fastq file starting point
R
crispr
fastq
7.4 years ago
kfburbach
• 0
2
votes
1
reply
1.3k
views
Uniting SRA Data into a single file
R
fastq
SRA
sradb
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
grecoandreauni
• 0
0
votes
2
replies
2.7k
views
subset from fastq file
fastq
7.6 years ago
KB
▴ 50
0
votes
1
reply
2.0k
views
Error downloading using SRAdb
fastq
sradb
ftp
updated 8.1 years ago by
Jack Zhu
▴ 170 • written 8.1 years ago by
yugi1001
• 0
1
vote
9
replies
2.7k
views
need help manipulating fastq file
fastq
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
KB
▴ 50
0
votes
2
replies
3.0k
views
Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
deseq2
deseqdataset
rnaseqgene
fastq
reference genome
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
greg.mulhearn
• 0
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread
fastq
9.0 years ago
danova_fr
▴ 20
5
votes
1
reply
3.1k
views
fastqSampler and writeFastq in shortread package
shortread
fastq
write
updated 9.2 years ago by
Martin Morgan
25k • written 9.2 years ago by
francesca.defilippis
▴ 100
22 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark
by
jacques.imbert
• 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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