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Showing :
questions
0
votes
0
replies
237
views
Strand inconsistency between Long read tool and minimap2?
minimap2
12 weeks ago by
shinyjj
▴ 50
2
votes
7
replies
666
views
How to check coverage in bam file?
bam
updated 3 months ago by
cmdcolin
★ 4.0k • written 3 months ago by
shinyjj
▴ 50
0
votes
3
replies
413
views
3 samples (control) vs 3 samples (condition) 100M coverage data
reads
updated 3 months ago by
Kevin Blighe
88k • written 3 months ago by
shinyjj
▴ 50
2
votes
1
reply
345
views
Quality check in long read (ONT, PacBio) bam files
QC
bam
minimap2
updated 3 months ago by
GenoMax
148k • written 3 months ago by
shinyjj
▴ 50
1
vote
8
replies
701
views
minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
minimap2
3 months ago by
shinyjj
▴ 50
4
votes
2
replies
5.7k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 8 months ago by
vague-barracuda-4686
• 0 • written 2.1 years ago by
shinyjj
▴ 50
0
votes
5
replies
928
views
Does salmon work with combined short and long read bam file?
salmon
updated 4 months ago by
callumjcparr
▴ 90 • written 10 months ago by
shinyjj
▴ 50
0
votes
2
replies
419
views
Question regarding transcript quantification with hybrid seq
short-read
salmon
long-read
hybrid-seq
updated 10 months ago by
jared.andrews07
★ 18k • written 10 months ago by
shinyjj
▴ 50
3
votes
3
replies
921
views
salmon with long reads
salmon
updated 11 months ago by
Rob
6.9k • written 11 months ago by
shinyjj
▴ 50
1
vote
2
replies
770
views
Visualize raw rna fastq file and aligned bam file
bam
genome
fastq
browser
updated 13 months ago by
Alex Reynolds
36k • written 13 months ago by
shinyjj
▴ 50
0
votes
0
replies
380
views
Count hexamer bias from pair end short read data
short
DESeq2
bias
read
hexamer
updated 18 months ago by
rpolicastro
13k • written 18 months ago by
shinyjj
▴ 50
2
votes
3
replies
990
views
rna long read length distibution
long-read
updated 8 months ago by
Ram
44k • written 19 months ago by
shinyjj
▴ 50
1
vote
1
reply
1.2k
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 8 months ago by
Ram
44k • written 19 months ago by
shinyjj
▴ 50
1
vote
3
replies
967
views
How does salmon uses polyester?
salmon
updated 19 months ago by
Michael Love
★ 2.6k • written 19 months ago by
shinyjj
▴ 50
5
votes
12
replies
2.6k
views
Mean read length from bam file
bam
samtools
updated 20 months ago by
seidel
11k • written 2.0 years ago by
shinyjj
▴ 50
1
vote
1
reply
620
views
intron retention length detected by short read > long read
intron-retention
updated 21 months ago by
LChart
4.7k • written 21 months ago by
shinyjj
▴ 50
4
votes
6
replies
2.0k
views
salmon output interpretation
salmon
updated 21 months ago by
GenoMax
148k • written 21 months ago by
shinyjj
▴ 50
13
votes
4
replies
3.3k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 8 months ago by
Ram
44k • written 21 months ago by
shinyjj
▴ 50
4
votes
3
replies
1.4k
views
Salmon TPM calculation constant
salmon
TPM
21 months ago by
shinyjj
▴ 50
0
votes
0
replies
571
views
Intron retention gene expression using salmon
salmon
intron-retention
updated 21 months ago by
Ram
44k • written 21 months ago by
shinyjj
▴ 50
2
votes
1
reply
1.1k
views
isoform compostion (psi) question
composition
isoform
updated 22 months ago by
i.sudbery
20k • written 22 months ago by
shinyjj
▴ 50
0
votes
2
replies
993
views
seqtk subsample fastq file question
seqtk
subsample
updated 23 months ago by
michael
▴ 10 • written 23 months ago by
shinyjj
▴ 50
2
votes
1
reply
638
views
STAR paired end mode question
STAR
updated 23 months ago by
ATpoint
86k • written 23 months ago by
shinyjj
▴ 50
1
vote
1
reply
819
views
qtl, eqtl, sqtl
eqtl
qtl
sqtl
updated 23 months ago by
acvill
▴ 350 • written 23 months ago by
shinyjj
▴ 50
0
votes
1
reply
548
views
Mean read length from a fastq file
fastq
samtools
awk
updated 21 months ago by
Ram
44k • written 23 months ago by
shinyjj
▴ 50
3
votes
3
replies
845
views
Subseq bam file
bam
subseq
updated 21 months ago by
Ram
44k • written 2.0 years ago by
shinyjj
▴ 50
0
votes
0
replies
402
views
Count splice junction reads from BED, bam, gtf file
splice
reads
junction
2.1 years ago by
shinyjj
▴ 50
0
votes
2
replies
692
views
bed file question! [extract read numbers from bed file]
BED
updated 21 months ago by
Ram
44k • written 2.1 years ago by
shinyjj
▴ 50
0
votes
0
replies
407
views
Count read numbers of splice junctions from BED file
BED
updated 21 months ago by
Ram
44k • written 2.1 years ago by
shinyjj
▴ 50
1
vote
4
replies
1.2k
views
Tools for fasterq file?
trimming
updated 2.1 years ago by
NikhilP
▴ 20 • written 2.1 years ago by
shinyjj
▴ 50
0
votes
4
replies
952
views
SRA: realistic data from reference transcript
reference
SRA
transcript
2.1 years ago by
shinyjj
▴ 50
0
votes
0
replies
471
views
Realistic RNA-seq using Polyester + Differences between Hexamer bias and positional bias?
polyester
short-read
bias
updated 8 months ago by
Ram
44k • written 2.1 years ago by
shinyjj
▴ 50
7
votes
9
replies
1.7k
views
Tools to check the length of isoforms in reference transcript
transcript
histogram
isoform
2.1 years ago by
shinyjj
▴ 50
2
votes
3
replies
1.3k
views
Tools for read length distribution
read-length
updated 2.2 years ago by
GenoMax
148k • written 2.2 years ago by
shinyjj
▴ 50
1
vote
4
replies
990
views
Tools for generating realistic rna-seq reads from reference transcriptome
reference
reads
rna-seq
transcriptome
2.2 years ago by
shinyjj
▴ 50
1
vote
2
replies
817
views
RefSeq Transcript vs Reference Genome sequence
Transcript
RefSeq
updated 2.2 years ago by
Jeremy
▴ 930 • written 2.2 years ago by
shinyjj
▴ 50
0
votes
5
replies
1.3k
views
Order of reads in Long read FASTQ file
fastq
seqtk
rna-seq
updated 2.2 years ago by
GenoMax
148k • written 2.2 years ago by
shinyjj
▴ 50
0
votes
0
replies
408
views
GTEx long read data
short-read
long-read
gtex
updated 8 months ago by
Ram
44k • written 2.2 years ago by
shinyjj
▴ 50
1
vote
1
reply
606
views
unsolved questions in RNA
isoform
rna
updated 2.2 years ago by
ATpoint
86k • written 2.2 years ago by
shinyjj
▴ 50
0
votes
1
reply
517
views
How to see maximal read length / average read length using STAR
STAR
updated 2.2 years ago by
Istvan Albert
102k • written 2.2 years ago by
shinyjj
▴ 50
0
votes
0
replies
355
views
Long read RNA # of reads interpretation help
nanopore
oxford
PacBio
2.2 years ago by
shinyjj
▴ 50
0
votes
0
replies
418
views
Coverage definition between DNA vs RNA
coverage
dna
rna
2.3 years ago by
shinyjj
▴ 50
0
votes
1
reply
602
views
Tools for generating realistic rna-seq reads
reads
RNA-seq
updated 2.2 years ago by
Ram
44k • written 2.3 years ago by
shinyjj
▴ 50
0
votes
3
replies
1.4k
views
How to calculate coverage in short-reads and long-reads in RNA-Seq?
rna-seq
short-read
long-read
updated 8 months ago by
Ram
44k • written 2.3 years ago by
shinyjj
▴ 50
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