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3
votes
5
replies
1.6k
views
Tools for fasterq file?
trimming
updated 12 weeks ago by ▴ 390 • written 2.5 years ago by ▴ 60
0
votes
0
replies
325
views
Strand inconsistency between Long read tool and minimap2?
minimap2
7 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 ★ 4.2k • written 8 months ago by ▴ 60
0
votes
2
replies
1.3k
views
Comment: Comment: How to check coverage in bam file?
8 months ago by shinyjj ▴ 60
0
votes
3
replies
718
views
3 samples (control) vs 3 samples (condition) 100M coverage data
reads
updated 8 months ago by 89k • written 8 months ago by ▴ 60
2
votes
1
reply
612
views
Quality check in long read (ONT, PacBio) bam files
QC bam minimap2
updated 8 months ago by 151k • written 8 months ago by ▴ 60
0
votes
0
replies
1.3k
views
Comment: Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
8 months ago by shinyjj ▴ 60
0
votes
1
reply
1.3k
views
Comment: Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
8 months ago by shinyjj ▴ 60
0
votes
1
reply
1.3k
views
Comment: Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
8 months ago by shinyjj ▴ 60
0
votes
1
reply
1.3k
views
Comment: Comment: minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
8 months ago by shinyjj ▴ 60
1
vote
8
replies
1.3k
views
minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
minimap2
8 months ago by shinyjj ▴ 60
4
votes
2
replies
7.6k
views
Genome annotation: convert gtf to gff3 file
gff3 gtf
updated 13 months ago by • 0 • written 2.5 years ago by ▴ 60
0
votes
5
replies
1.2k
views
Does salmon work with combined short and long read bam file?
salmon
updated 9 months ago by ▴ 90 • written 15 months ago by ▴ 60
0
votes
2
replies
533
views
Question regarding transcript quantification with hybrid seq
short-read salmon long-read hybrid-seq
updated 15 months ago by ★ 18k • written 15 months ago by ▴ 60
0
votes
0
replies
1.2k
views
Comment: Comment: Does salmon work with combined short and long read bam file?
15 months ago by shinyjj ▴ 60
0
votes
1
reply
1.4k
views
Comment: Comment: salmon with long reads
16 months ago by shinyjj ▴ 60
5
votes
3
replies
1.4k
views
salmon with long reads
salmon
updated 16 months ago by 7.1k • written 16 months ago by ▴ 60
1
vote
2
replies
992
views
Visualize raw rna fastq file and aligned bam file
bam genome fastq browser
updated 18 months ago by 36k • written 18 months ago by ▴ 60
0
votes
0
replies
485
views
Count hexamer bias from pair end short read data
short DESeq2 bias read hexamer
updated 23 months ago by 13k • written 23 months ago by ▴ 60
0
votes
1
reply
1.2k
views
Comment: Comment: rna long read length distibution
24 months ago by shinyjj ▴ 60
2
votes
3
replies
1.2k
views
rna long read length distibution
long-read
updated 13 months ago by 45k • written 24 months ago by ▴ 60
1
vote
1
reply
1.4k
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 45k • written 24 months ago by ▴ 60
0
votes
1
reply
1.2k
views
Comment: Comment: How does salmon uses polyester?
2.0 years ago by shinyjj ▴ 60
1
vote
3
replies
1.2k
views
How does salmon uses polyester?
salmon
updated 2.0 years ago by ★ 2.6k • written 2.0 years ago by ▴ 60
5
votes
12
replies
3.1k
views
Mean read length from bam file
bam samtools
updated 2.1 years ago by 11k • written 2.4 years ago by ▴ 60
1
vote
1
reply
765
views
intron retention length detected by short read > long read
intron-retention
updated 2.2 years ago by 4.9k • written 2.2 years ago by ▴ 60
0
votes
0
replies
2.6k
views
Comment: Comment: salmon output interpretation
2.2 years ago by shinyjj ▴ 60
4
votes
6
replies
2.6k
views
salmon output interpretation
salmon
updated 2.2 years ago by 151k • written 2.2 years ago by ▴ 60
0
votes
0
replies
2.6k
views
Comment: Comment: salmon output interpretation
updated 2.2 years ago by 151k • written 2.2 years ago by ▴ 60
0
votes
1
reply
2.6k
views
Comment: Comment: salmon output interpretation
2.2 years ago by shinyjj ▴ 60
13
votes
4
replies
4.0k
views
long read + salmon? (transcript abundance)
long-read salmon
updated 13 months ago by 45k • written 2.2 years ago by ▴ 60
0
votes
0
replies
1.7k
views
Comment: Comment: Salmon TPM calculation constant
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
664
views
Intron retention gene expression using salmon
salmon intron-retention
updated 2.2 years ago by 45k • written 2.2 years ago by ▴ 60
3
votes
1
reply
1.5k
views
isoform compostion (psi) question
composition isoform
updated 2.3 years ago by 21k • written 2.3 years ago by ▴ 60
0
votes
2
replies
1.2k
views
seqtk subsample fastq file question
seqtk subsample
updated 2.3 years ago by ▴ 10 • written 2.3 years ago by ▴ 60
0
votes
0
replies
1.2k
views
Comment: Comment: seqtk subsample fastq file question
2.3 years ago by shinyjj ▴ 60
2
votes
1
reply
707
views
STAR paired end mode question
STAR
updated 2.3 years ago by 88k • written 2.3 years ago by ▴ 60
1
vote
1
reply
997
views
qtl, eqtl, sqtl
eqtl qtl sqtl
updated 2.3 years ago by ▴ 350 • written 2.3 years ago by ▴ 60
0
votes
1
reply
643
views
Mean read length from a fastq file
fastq samtools awk
updated 2.1 years ago by 45k • written 2.3 years ago by ▴ 60
0
votes
1
reply
969
views
Comment: Comment: Subseq bam file
2.4 years ago by shinyjj ▴ 60
3
votes
3
replies
969
views
Subseq bam file
bam subseq
updated 2.1 years ago by 45k • written 2.4 years ago by ▴ 60
0
votes
1
reply
3.1k
views
Comment: Comment: Mean read length from bam file
2.4 years ago by shinyjj ▴ 60
0
votes
1
reply
3.1k
views
Comment: Comment: Mean read length from bam file
2.4 years ago by shinyjj ▴ 60
0
votes
1
reply
3.1k
views
Comment: Comment: Mean read length from bam file
2.4 years ago by shinyjj ▴ 60
0
votes
1
reply
3.1k
views
Comment: Comment: Mean read length from bam file
2.4 years ago by shinyjj ▴ 60
0
votes
0
replies
467
views
Count splice junction reads from BED, bam, gtf file
splice reads junction
2.5 years ago by shinyjj ▴ 60
0
votes
0
replies
815
views
Comment: Comment: bed file question! [extract read numbers from bed file]
2.5 years ago by shinyjj ▴ 60
0
votes
2
replies
815
views
bed file question! [extract read numbers from bed file]
BED
updated 2.1 years ago by 45k • written 2.5 years ago by ▴ 60
0
votes
0
replies
459
views
Count read numbers of splice junctions from BED file
BED
updated 2.1 years ago by 45k • written 2.5 years ago by ▴ 60
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