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4
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115
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Can Salmon's quantification method accommodate concatenated reads of varying length (from independent sequencers) in a single fastq file?
salmon rna-seq sequencing written 19 days ago by c_dampier • 50
0
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0
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81
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0
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can't find why certain reads are unmapped by salmon
salmon rna-seq written 21 days ago by vaushev • 10
7
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1
answer
204
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1
answer
Salmon Counts differ in Alignment and Quasi-Mapping mode
alignment salmon rna-seq written 5 weeks ago by MaxF • 10
2
votes
1
answer
95
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1
answer
Highly uneven RINs, mapping rates, and methods to deal with this (normalisation, salmon)
salmon rna-seq normalisation written 6 weeks ago by chris86 • 240
1
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132
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0
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Salmon: Any downstream DEA tools which uses abundance estimate variation information?
deseq2 salmon written 6 weeks ago by Thomas • 90
4
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1
answer
134
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1
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What transcript quantification tool would you recommend for 3' prime RNA-seq?
transcript quantification salmon rna-seq written 8 weeks ago by roy.granit • 790 • updated 8 weeks ago by WouterDeCoster ♦ 37k
0
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144
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how do normalization for transcript length
tximport transcript coverage salmon plot written 9 weeks ago by lkianmehr • 30
0
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0
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117
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0
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Hypsibius dujardini locus ID conversion
alignment salmon rna-seq written 3 months ago by stanley.ju • 0
0
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1
answer
342
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5 follow
1
answer
FASTQ alignment result is really bad
htseq-count salmon rna-seq written 3 months ago by bharata1803 • 420 • updated 3 months ago by h.mon ♦ 24k
0
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199
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0
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repeatmask fasta file
teelements salmon repeatmask index written 4 months ago by lkianmehr • 30 • updated 4 months ago by Biostar ♦♦ 20
0
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1
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1.2k
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1
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What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?
sleuth salmon kallisto rna-seq dte written 2.2 years ago by james.lloyd • 80 • updated 4 months ago by lalvarez • 10
1
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2
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198
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2
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May I use numreads for doing DGE after quantifying by Salmon
salmon dge written 4 months ago by lkianmehr • 30 • updated 4 months ago by WouterDeCoster ♦ 37k
0
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0
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293
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0
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salmon - tximport - deseq2 gene level workflow
tximport deseq2 salmon rna-seq written 4 months ago by jomo018 • 470
2
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2
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276
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2
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rRNA removal needed for salmon / DESeq2 analysis
rrna deseq2 salmon contamination written 4 months ago by mark.dunning • 200
3
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1
answer
386
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1
answer
Bash: salmon command not found
salmon rna-seq bash written 4 months ago by ab123 • 40
5
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2
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333
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6 follow
2
answers
Average Insert Size When Using Transcript Quantification Tools Such as Salmon?
next-gen salmon rna-seq written 4 months ago by Dru Zod • 0 • updated 4 months ago by Rob ♦ 3.2k
3
votes
1
answer
356
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1
answer
Alignment-free tools (like Kallisto or Salmon): useful for bacterial transcriptomes?
bacteria salmon rna-seq written 4 months ago by arctan • 0 • updated 4 months ago by Istvan Albert ♦♦ 79k
3
votes
1
answer
390
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1
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Orientation of reads in .fastq files from RNA-Seq
salmon rna-seq written 5 months ago by newbio17 • 10 • updated 5 months ago by swbarnes2 ♦ 5.0k
4
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2
answers
580
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2
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Salmon (error: SAM file and fasta file have different transcript length)
salmon rna-seq written 5 months ago by shivyasoni1994 • 0 • updated 5 months ago by jomo018 • 470
1
vote
1
answer
311
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1
answer
Salmon error message
salmon rna-seq written 5 months ago by saadleeshehreen • 60 • updated 5 months ago by Devon Ryan ♦ 88k
3
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0
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506
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0
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how do Differential gene expression analysis by Salmon output
salmon differential gene expression written 5 months ago by lkianmehr • 30 • updated 5 months ago by genomax ♦ 64k
3
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1
answer
248
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1
answer
Interpretation of Salmon quat.sf result
salmon rna-seq written 5 months ago by saadleeshehreen • 60 • updated 5 months ago by h.mon ♦ 24k
1
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0
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1.4k
views
0
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Salmon very low mapping
salmon rna-seq written 16 months ago by Tania • 120 • updated 5 months ago by Biostar ♦♦ 20
3
votes
1
answer
303
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1
answer
Will Kallisto or Salmon perform streaming alignment from the Sequence Read Archive?
pseudoaligners salmon kallisto written 6 months ago by b10hazard • 20 • updated 6 months ago by RamRS ♦ 20k
12
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2
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615
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2
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Salmon Quantification for RNA-seq Read Pairs with Different Lengths
quantification salmon rna-seq written 6 months ago by ATpoint ♦ 14k
5
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2
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360
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2
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Salmon quantification vs HTSeq count quantification
htseq-count salmon written 6 months ago by vincentpailler • 50 • updated 6 months ago by h.mon ♦ 24k
3
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1
answer
280
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1
answer
Salmon Algorithm Binary Search
salmon written 7 months ago by vincentpailler • 50 • updated 7 months ago by Rob ♦ 3.2k
11
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1
answer
1.1k
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6 follow
1
answer
Mapping vs Quasi-Mapping
salmon quasi-mapping written 7 months ago by vincentpailler • 50
4
votes
1
answer
657
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1
answer
Difference between HTSeq-count & Salmon quant results
htseq-count salmon rna-seq written 7 months ago by vincentpailler • 50 • updated 7 months ago by genomax ♦ 64k
2
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1
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380
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1
answer
Salmon / IGV
salmon igv written 7 months ago by vincentpailler • 50 • updated 7 months ago by h.mon ♦ 24k
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