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3
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1
answer
743
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1
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Library type warning in Salmon
rnaseq salmon library-type written 22 months ago by grant.hovhannisyan • 1.9k • updated 4 days ago by Biostar ♦♦ 20
2
votes
1
answer
54
views
1
answer
Salmon annotation of transcripts in quasi-mapping step
salmon mapping pseudoalignment written 9 days ago by Iara Souza • 0 • updated 9 days ago by Devon Ryan ♦ 94k
0
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0
answers
71
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0
answers
Issue with Salmon and Deseq2 with paired-end and single-end reads libraries
rnaseq tximport deseq2 salmon written 14 days ago by Andrés Ribone • 0
3
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0
answers
128
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0
answers
Salmon only processes human reads from PDX data
software error alignment salmon rna-seq written 27 days ago by jrleary • 60
0
votes
0
answers
126
views
0
answers
salmon quantification vs. star mapping
alignment salmon star mapping written 6 weeks ago by Assa Yeroslaviz • 1.3k
1
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1
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152
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1
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Salmon auxiliary output
salmon written 4 months ago by g.wang2 • 0 • updated 10 weeks ago by Ahill • 1.8k
4
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1
answer
744
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1
answer
rRNA removal needed for salmon / DESeq2 analysis
rrna deseq2 salmon contamination written 15 months ago by mark.dunning • 210 • updated 11 weeks ago by ATpoint ♦ 29k
0
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0
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183
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0
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Salmon RNA-seq quantification for repeated genome
salmon rna-seq written 3 months ago by jordi.planells • 90
4
votes
1
answer
208
views
1
answer
BWA-MEM versus Salmon - how to interpret large differences between read outputs
bwa-mem alignment salmon deseq2 rna-seq written 3 months ago by gmchaput • 10 • updated 3 months ago by ATpoint ♦ 29k
1
vote
1
answer
800
views
6 follow
1
answer
Salmon error message
salmon rna-seq written 16 months ago by saadleeshehreen • 70 • updated 3 months ago by mr.udvr • 20
6
votes
1
answer
263
views
5 follow
1
answer
salmon was only able to assign 0 fragments to transcripts
windows10 salmon docker rna-seq written 4 months ago by naseerkhan861 • 0 • updated 4 months ago by yztxwd • 290
0
votes
0
answers
940
views
5 follow
0
answers
How to add tdtomato to mouse genome for RNA seq analysis
salmon rna-seq written 22 months ago by jevanveen • 20 • updated 4 months ago by findingdan • 0
0
votes
0
answers
143
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0
answers
How does Salmon handle reads that map to multiple locations that each have full coverage?
dea salmon mapping rna-seq written 5 months ago by cameron.holman • 0
3
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0
answers
141
views
0
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News: Testing and feedback of upcoming salmon release
news salmon rna-seq written 5 months ago by Rob ♦ 3.7k
1
vote
1
answer
580
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1
answer
Generate gene level TPM from quant.sf file generated in salmon
R txtimport salmon rna-seq tpm written 5 months ago by pyrhana25 • 0 • updated 5 months ago by i.sudbery ♦ 7.0k
4
votes
1
answer
452
views
1
answer
Adapter trimming before mapping with Salmon
adapters salmon rna-seq written 5 months ago by justinjacobse • 0 • updated 5 months ago by igor ♦ 9.6k
4
votes
2
answers
440
views
2
answers
Salmon tximport get TPM
salmon rna-seq written 5 months ago by bharata1803 • 450
1
vote
0
answers
404
views
0
answers
rna-seq analysis with Salmon - how to Import and summarize using tximport
tximport salmon rna-seq written 6 months ago by woojoy14 • 0
6
votes
0
answers
339
views
0
answers
Merging the output of salmon for RNA-seq counting with paired-end and single-end reads simultaneously
paired-end salmon rna-seq single-end written 6 months ago by nanoide • 40
0
votes
1
answer
288
views
1
answer
Can you choose minimum transcript coverage in salmon
salmon rna-seq written 6 months ago by yryan • 0 • updated 6 months ago by kristoffer.vittingseerup • 3.0k
4
votes
1
answer
303
views
5 follow
1
answer
Salmon GC bias with caution
salmon rna-seq written 6 months ago by Morris_Chair • 170 • updated 6 months ago by h.mon ♦ 29k
0
votes
0
answers
181
views
0
answers
Mapping a list of sequences to gene symbol
stringtie salmon htseqcount hisat2 written 7 months ago by catechize.2.learn • 110
0
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0
answers
225
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0
answers
Counting Ribo-seq data on gene and transcript level?
riboseq salmon featurecounts rna-seq written 7 months ago by BPors • 40
0
votes
0
answers
358
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5 follow
0
answers
salmon NumReads inconsistent with depth from --writeMappings?
software error R salmon samtools rna-seq written 7 months ago by ningyuan.sg • 0
1
vote
1
answer
185
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1
answer
Is there Quality score/measure to compare salmon results using different kmer values?
salmon rna-seq written 7 months ago by karni_bedirian • 0 • updated 7 months ago by ATpoint ♦ 29k
2
votes
1
answer
332
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1
answer
Does salmon use phred scores while pseudoaligning (and/or validating mapping)?
salmon phred written 9 months ago by Anthony • 0 • updated 7 months ago by karni_bedirian • 0
4
votes
1
answer
266
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5 follow
1
answer
Comparing different transcripts expression level of a list of genes from one condition
R deseq2 salmon kallisto rna-seq written 7 months ago by mr.monahton • 20 • updated 7 months ago by andrew.j.skelton73 ♦ 5.9k
0
votes
1
answer
255
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1
answer
Use Salmon to annotate a Sam file
alignment quantification salmon rna-seq written 7 months ago by Florian Bernard • 70 • updated 7 months ago by ATpoint ♦ 29k
6
votes
1
answer
348
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1
answer
Where can I download the Danio Rerio (zebrafish) transcriptome?
zebrafish salmon rna-seq genomics transcriptome written 8 months ago by dtatarak • 10 • updated 7 months ago by Biostar ♦♦ 20
5
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0
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424
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0
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Which bias flags to run with Salmon before DESeq2 analysis?
deseq2 salmon bias flags rna-seq written 8 months ago by cameron.holman • 0
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