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Showing :
questions
3
votes
5
replies
1.6k
views
Tools for fasterq file?
trimming
updated 3 months ago by
AB
▴ 390 • written 2.5 years ago by
shinyjj
▴ 60
0
votes
0
replies
329
views
Strand inconsistency between Long read tool and minimap2?
minimap2
8 months ago by
shinyjj
▴ 60
2
votes
7
replies
1.3k
views
How to check coverage in bam file?
bam
updated 8 months ago by
cmdcolin
★ 4.2k • written 8 months ago by
shinyjj
▴ 60
0
votes
3
replies
732
views
3 samples (control) vs 3 samples (condition) 100M coverage data
reads
updated 8 months ago by
Kevin Blighe
89k • written 8 months ago by
shinyjj
▴ 60
2
votes
1
reply
626
views
Quality check in long read (ONT, PacBio) bam files
QC
bam
minimap2
updated 9 months ago by
GenoMax
151k • written 9 months ago by
shinyjj
▴ 60
1
vote
8
replies
1.4k
views
minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
minimap2
9 months ago by
shinyjj
▴ 60
4
votes
2
replies
7.7k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 14 months ago by
vague-barracuda-4686
• 0 • written 2.5 years ago by
shinyjj
▴ 60
0
votes
5
replies
1.3k
views
Does salmon work with combined short and long read bam file?
salmon
updated 10 months ago by
callumjcparr
▴ 90 • written 15 months ago by
shinyjj
▴ 60
0
votes
2
replies
540
views
Question regarding transcript quantification with hybrid seq
short-read
salmon
long-read
hybrid-seq
updated 15 months ago by
jared.andrews07
★ 18k • written 15 months ago by
shinyjj
▴ 60
5
votes
3
replies
1.5k
views
salmon with long reads
salmon
updated 16 months ago by
Rob
7.1k • written 16 months ago by
shinyjj
▴ 60
1
vote
2
replies
1.0k
views
Visualize raw rna fastq file and aligned bam file
bam
genome
fastq
browser
updated 19 months ago by
Alex Reynolds
36k • written 19 months ago by
shinyjj
▴ 60
0
votes
0
replies
489
views
Count hexamer bias from pair end short read data
short
DESeq2
bias
read
hexamer
updated 23 months ago by
rpolicastro
13k • written 23 months ago by
shinyjj
▴ 60
2
votes
3
replies
1.2k
views
rna long read length distibution
long-read
updated 13 months ago by
Ram
45k • written 2.0 years ago by
shinyjj
▴ 60
1
vote
1
reply
1.5k
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 13 months ago by
Ram
45k • written 2.0 years ago by
shinyjj
▴ 60
1
vote
3
replies
1.3k
views
How does salmon uses polyester?
salmon
updated 2.0 years ago by
Michael Love
★ 2.6k • written 2.0 years ago by
shinyjj
▴ 60
5
votes
12
replies
3.1k
views
Mean read length from bam file
bam
samtools
updated 2.1 years ago by
seidel
11k • written 2.5 years ago by
shinyjj
▴ 60
1
vote
1
reply
774
views
intron retention length detected by short read > long read
intron-retention
updated 2.2 years ago by
LChart
4.9k • written 2.2 years ago by
shinyjj
▴ 60
4
votes
6
replies
2.6k
views
salmon output interpretation
salmon
updated 2.2 years ago by
GenoMax
151k • written 2.2 years ago by
shinyjj
▴ 60
13
votes
4
replies
4.1k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 13 months ago by
Ram
45k • written 2.2 years ago by
shinyjj
▴ 60
4
votes
3
replies
1.7k
views
Salmon TPM calculation constant
salmon
TPM
2.2 years ago by
shinyjj
▴ 60
0
votes
0
replies
669
views
Intron retention gene expression using salmon
salmon
intron-retention
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
shinyjj
▴ 60
3
votes
1
reply
1.6k
views
isoform compostion (psi) question
composition
isoform
updated 2.3 years ago by
i.sudbery
21k • written 2.3 years ago by
shinyjj
▴ 60
0
votes
2
replies
1.2k
views
seqtk subsample fastq file question
seqtk
subsample
updated 2.3 years ago by
michael
▴ 10 • written 2.3 years ago by
shinyjj
▴ 60
2
votes
1
reply
712
views
STAR paired end mode question
STAR
updated 2.3 years ago by
ATpoint
88k • written 2.3 years ago by
shinyjj
▴ 60
1
vote
1
reply
1.0k
views
qtl, eqtl, sqtl
eqtl
qtl
sqtl
updated 2.3 years ago by
acvill
▴ 350 • written 2.3 years ago by
shinyjj
▴ 60
0
votes
1
reply
648
views
Mean read length from a fastq file
fastq
samtools
awk
updated 2.2 years ago by
Ram
45k • written 2.4 years ago by
shinyjj
▴ 60
3
votes
3
replies
978
views
Subseq bam file
bam
subseq
updated 2.2 years ago by
Ram
45k • written 2.5 years ago by
shinyjj
▴ 60
0
votes
0
replies
469
views
Count splice junction reads from BED, bam, gtf file
splice
reads
junction
2.5 years ago by
shinyjj
▴ 60
0
votes
2
replies
822
views
bed file question! [extract read numbers from bed file]
BED
updated 2.2 years ago by
Ram
45k • written 2.5 years ago by
shinyjj
▴ 60
0
votes
0
replies
463
views
Count read numbers of splice junctions from BED file
BED
updated 2.2 years ago by
Ram
45k • written 2.5 years ago by
shinyjj
▴ 60
0
votes
4
replies
1.2k
views
SRA: realistic data from reference transcript
reference
SRA
transcript
2.5 years ago by
shinyjj
▴ 60
0
votes
0
replies
571
views
Realistic RNA-seq using Polyester + Differences between Hexamer bias and positional bias?
polyester
short-read
bias
updated 13 months ago by
Ram
45k • written 2.6 years ago by
shinyjj
▴ 60
7
votes
9
replies
2.0k
views
Tools to check the length of isoforms in reference transcript
transcript
histogram
isoform
2.6 years ago by
shinyjj
▴ 60
2
votes
3
replies
1.7k
views
Tools for read length distribution
read-length
updated 2.6 years ago by
GenoMax
151k • written 2.6 years ago by
shinyjj
▴ 60
1
vote
4
replies
1.2k
views
Tools for generating realistic rna-seq reads from reference transcriptome
reference
reads
rna-seq
transcriptome
2.6 years ago by
shinyjj
▴ 60
1
vote
2
replies
990
views
RefSeq Transcript vs Reference Genome sequence
Transcript
RefSeq
updated 2.6 years ago by
Jeremy
▴ 930 • written 2.6 years ago by
shinyjj
▴ 60
0
votes
5
replies
1.6k
views
Order of reads in Long read FASTQ file
fastq
seqtk
rna-seq
updated 2.6 years ago by
GenoMax
151k • written 2.6 years ago by
shinyjj
▴ 60
0
votes
0
replies
494
views
GTEx long read data
short-read
long-read
gtex
updated 13 months ago by
Ram
45k • written 2.6 years ago by
shinyjj
▴ 60
1
vote
1
reply
691
views
unsolved questions in RNA
isoform
rna
updated 2.7 years ago by
ATpoint
88k • written 2.7 years ago by
shinyjj
▴ 60
0
votes
1
reply
626
views
How to see maximal read length / average read length using STAR
STAR
updated 2.7 years ago by
Istvan Albert
102k • written 2.7 years ago by
shinyjj
▴ 60
0
votes
0
replies
415
views
Long read RNA # of reads interpretation help
nanopore
oxford
PacBio
2.7 years ago by
shinyjj
▴ 60
0
votes
0
replies
486
views
Coverage definition between DNA vs RNA
coverage
dna
rna
2.7 years ago by
shinyjj
▴ 60
0
votes
1
reply
689
views
Tools for generating realistic rna-seq reads
reads
RNA-seq
updated 2.6 years ago by
Ram
45k • written 2.7 years ago by
shinyjj
▴ 60
0
votes
3
replies
1.7k
views
How to calculate coverage in short-reads and long-reads in RNA-Seq?
rna-seq
short-read
long-read
updated 13 months ago by
Ram
45k • written 2.7 years ago by
shinyjj
▴ 60
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