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comments
0
votes
0
replies
226
views
Strand inconsistency between Long read tool and minimap2?
minimap2
9 weeks ago by
shinyjj
▴ 50
2
votes
7
replies
622
views
How to check coverage in bam file?
bam
updated 12 weeks ago by
cmdcolin
★ 4.0k • written 12 weeks ago by
shinyjj
▴ 50
0
votes
2
replies
622
views
Comment:
Comment: How to check coverage in bam file?
12 weeks ago by
shinyjj
▴ 50
0
votes
3
replies
390
views
3 samples (control) vs 3 samples (condition) 100M coverage data
reads
updated 12 weeks ago by
Kevin Blighe
88k • written 12 weeks ago by
shinyjj
▴ 50
2
votes
1
reply
319
views
Quality check in long read (ONT, PacBio) bam files
QC
bam
minimap2
updated 3 months ago by
GenoMax
147k • written 3 months ago by
shinyjj
▴ 50
0
votes
0
replies
637
views
Comment:
Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
3 months ago by
shinyjj
▴ 50
0
votes
1
reply
637
views
Comment:
Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
3 months ago by
shinyjj
▴ 50
0
votes
1
reply
637
views
Comment:
Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
3 months ago by
shinyjj
▴ 50
0
votes
1
reply
637
views
Comment:
Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
3 months ago by
shinyjj
▴ 50
1
vote
8
replies
637
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
5.5k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 8 months ago by
vague-barracuda-4686
• 0 • written 2.0 years ago by
shinyjj
▴ 50
0
votes
5
replies
904
views
Does salmon work with combined short and long read bam file?
salmon
updated 4 months ago by
callumjcparr
▴ 90 • written 9 months ago by
shinyjj
▴ 50
0
votes
2
replies
412
views
Question regarding transcript quantification with hybrid seq
short-read
salmon
long-read
hybrid-seq
updated 9 months ago by
jared.andrews07
★ 18k • written 9 months ago by
shinyjj
▴ 50
0
votes
0
replies
904
views
Comment:
Comment: Does salmon work with combined short and long read bam file?
9 months ago by
shinyjj
▴ 50
0
votes
1
reply
883
views
Comment:
Comment: salmon with long reads
10 months ago by
shinyjj
▴ 50
3
votes
3
replies
883
views
salmon with long reads
salmon
updated 10 months ago by
Rob
6.9k • written 10 months ago by
shinyjj
▴ 50
1
vote
2
replies
738
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
373
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
0
votes
1
reply
969
views
Comment:
Comment: rna long read length distibution
18 months ago by
shinyjj
▴ 50
2
votes
3
replies
969
views
rna long read length distibution
long-read
updated 7 months ago by
Ram
44k • written 18 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 7 months ago by
Ram
44k • written 18 months ago by
shinyjj
▴ 50
0
votes
1
reply
955
views
Comment:
Comment: How does salmon uses polyester?
18 months ago by
shinyjj
▴ 50
1
vote
3
replies
955
views
How does salmon uses polyester?
salmon
updated 18 months ago by
Michael Love
★ 2.6k • written 18 months ago by
shinyjj
▴ 50
5
votes
12
replies
2.5k
views
Mean read length from bam file
bam
samtools
updated 19 months ago by
seidel
11k • written 23 months ago by
shinyjj
▴ 50
1
vote
1
reply
605
views
intron retention length detected by short read > long read
intron-retention
updated 20 months ago by
LChart
4.5k • written 20 months ago by
shinyjj
▴ 50
0
votes
0
replies
2.0k
views
Comment:
Comment: salmon output interpretation
20 months ago by
shinyjj
▴ 50
4
votes
6
replies
2.0k
views
salmon output interpretation
salmon
updated 20 months ago by
GenoMax
147k • written 20 months ago by
shinyjj
▴ 50
0
votes
0
replies
2.0k
views
Comment:
Comment: salmon output interpretation
updated 20 months ago by
GenoMax
147k • written 20 months ago by
shinyjj
▴ 50
0
votes
1
reply
2.0k
views
Comment:
Comment: salmon output interpretation
20 months ago by
shinyjj
▴ 50
13
votes
4
replies
3.2k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 7 months ago by
Ram
44k • written 21 months ago by
shinyjj
▴ 50
0
votes
0
replies
1.3k
views
Comment:
Comment: Salmon TPM calculation constant
21 months ago by
shinyjj
▴ 50
4
votes
3
replies
1.3k
views
Salmon TPM calculation constant
salmon
TPM
21 months ago by
shinyjj
▴ 50
0
votes
0
replies
560
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
976
views
seqtk subsample fastq file question
seqtk
subsample
updated 22 months ago by
michael
▴ 10 • written 22 months ago by
shinyjj
▴ 50
0
votes
0
replies
976
views
Comment:
Comment: seqtk subsample fastq file question
22 months ago by
shinyjj
▴ 50
2
votes
1
reply
633
views
STAR paired end mode question
STAR
updated 22 months ago by
ATpoint
85k • written 22 months ago by
shinyjj
▴ 50
1
vote
1
reply
809
views
qtl, eqtl, sqtl
eqtl
qtl
sqtl
updated 22 months ago by
acvill
▴ 350 • written 22 months ago by
shinyjj
▴ 50
0
votes
1
reply
538
views
Mean read length from a fastq file
fastq
samtools
awk
updated 20 months ago by
Ram
44k • written 22 months ago by
shinyjj
▴ 50
0
votes
1
reply
833
views
Comment:
Comment: Subseq bam file
23 months ago by
shinyjj
▴ 50
3
votes
3
replies
833
views
Subseq bam file
bam
subseq
updated 20 months ago by
Ram
44k • written 23 months ago by
shinyjj
▴ 50
0
votes
1
reply
2.5k
views
Comment:
Comment: Mean read length from bam file
23 months ago by
shinyjj
▴ 50
0
votes
1
reply
2.5k
views
Comment:
Comment: Mean read length from bam file
23 months ago by
shinyjj
▴ 50
0
votes
1
reply
2.5k
views
Comment:
Comment: Mean read length from bam file
23 months ago by
shinyjj
▴ 50
0
votes
1
reply
2.5k
views
Comment:
Comment: Mean read length from bam file
23 months ago by
shinyjj
▴ 50
0
votes
0
replies
396
views
Count splice junction reads from BED, bam, gtf file
splice
reads
junction
2.0 years ago by
shinyjj
▴ 50
0
votes
0
replies
683
views
Comment:
Comment: bed file question! [extract read numbers from bed file]
2.0 years ago by
shinyjj
▴ 50
0
votes
2
replies
683
views
bed file question! [extract read numbers from bed file]
BED
updated 20 months ago by
Ram
44k • written 2.0 years ago by
shinyjj
▴ 50
0
votes
0
replies
402
views
Count read numbers of splice junctions from BED file
BED
updated 20 months ago by
Ram
44k • written 2.1 years ago by
shinyjj
▴ 50
0
votes
1
reply
1.1k
views
Comment:
Comment: Tools for fasterq file?
2.1 years ago by
shinyjj
▴ 50
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