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4
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1
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131
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1
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BWA-MEM versus Salmon - how to interpret large differences between read outputs
bwa-mem alignment salmon deseq2 rna-seq written 11 days ago by gmchaput • 10 • updated 11 days ago by ATpoint ♦ 25k
1
vote
1
answer
639
views
6 follow
1
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Salmon error message
salmon rna-seq written 13 months ago by saadleeshehreen • 70 • updated 15 days ago by mr.udvr • 20
6
votes
1
answer
127
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5 follow
1
answer
salmon was only able to assign 0 fragments to transcripts
windows10 salmon docker rna-seq written 19 days ago by naseerkhan861 • 0 • updated 19 days ago by yztxwd • 160
0
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0
answers
97
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0
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Salmon auxiliary output
salmon written 25 days ago by g.wang2 • 0
0
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0
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807
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5 follow
0
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How to add tdtomato to mouse genome for RNA seq analysis
salmon rna-seq written 19 months ago by jevanveen • 20 • updated 4 weeks ago by findingdan • 0
0
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0
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92
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0
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How does Salmon handle reads that map to multiple locations that each have full coverage?
dea salmon mapping rna-seq written 8 weeks ago by cameron.holman • 0
3
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0
answers
98
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0
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News: Testing and feedback of upcoming salmon release
news salmon rna-seq written 8 weeks ago by Rob ♦ 3.6k
1
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1
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472
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1
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Generate gene level TPM from quant.sf file generated in salmon
R txtimport salmon rna-seq tpm written 9 weeks ago by pyrhana25 • 0 • updated 9 weeks ago by i.sudbery ♦ 6.2k
4
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1
answer
236
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1
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Adapter trimming before mapping with Salmon
adapters salmon rna-seq written 9 weeks ago by justinjacobse • 0 • updated 9 weeks ago by igor ♦ 8.8k
3
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1
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196
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1
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Salmon tximport get TPM
salmon rna-seq written 10 weeks ago by bharata1803 • 430
1
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0
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198
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0
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rna-seq analysis with Salmon - how to Import and summarize using tximport
tximport salmon rna-seq written 11 weeks ago by woojoy14 • 0
6
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0
answers
194
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0
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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 11 weeks ago by nanoide • 30
0
votes
1
answer
236
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1
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Can you choose minimum transcript coverage in salmon
salmon rna-seq written 12 weeks ago by yryan • 0 • updated 11 weeks ago by kristoffer.vittingseerup • 2.6k
4
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1
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224
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5 follow
1
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Salmon GC bias with caution
salmon rna-seq written 12 weeks ago by Morris_Chair • 150 • updated 12 weeks ago by h.mon ♦ 28k
0
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0
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138
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0
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Mapping a list of sequences to gene symbol
stringtie salmon htseqcount hisat2 written 3 months ago by catechize.2.learn • 110
0
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0
answers
151
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0
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Counting Ribo-seq data on gene and transcript level?
riboseq salmon featurecounts rna-seq written 4 months ago by BPors • 40
0
votes
0
answers
291
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5 follow
0
answers
salmon NumReads inconsistent with depth from --writeMappings?
software error R salmon samtools rna-seq written 4 months ago by ningyuan.sg • 0
1
vote
1
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140
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1
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Is there Quality score/measure to compare salmon results using different kmer values?
salmon rna-seq written 4 months ago by karni_bedirian • 0 • updated 4 months ago by ATpoint ♦ 25k
3
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1
answer
260
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5 follow
1
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Does salmon use phred scores while pseudoaligning (and/or validating mapping)?
salmon phred written 6 months ago by Anthony • 0 • updated 4 months ago by karni_bedirian • 0
4
votes
1
answer
199
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5 follow
1
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Comparing different transcripts expression level of a list of genes from one condition
R deseq2 salmon kallisto rna-seq written 4 months ago by mr.monahton • 20 • updated 4 months ago by andrew.j.skelton73 ♦ 5.8k
0
votes
1
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195
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1
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Use Salmon to annotate a Sam file
alignment quantification salmon rna-seq written 4 months ago by Florian Bernard • 60 • updated 4 months ago by ATpoint ♦ 25k
6
votes
1
answer
239
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1
answer
Where can I download the Danio Rerio (zebrafish) transcriptome?
zebrafish salmon rna-seq genomics transcriptome written 4 months ago by dtatarak • 10 • updated 4 months ago by Biostar ♦♦ 20
5
votes
0
answers
322
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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 4 months ago by cameron.holman • 0
3
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0
answers
259
views
0
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Salmon quasi Index upgrade
salmon rna-seq written 5 months ago by Morris_Chair • 150 • updated 5 months ago by RamRS ♦ 24k
4
votes
1
answer
339
views
1
answer
How to build a transcriptome reference ?
salmon rna-seq written 5 months ago by darbinator • 190
8
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1
answer
443
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1
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Ensembl gene annotation GRCh37.87
ensembl salmon rna-seq written 7 months ago by A • 3.6k • updated 7 months ago by genomax ♦ 74k
2
votes
0
answers
461
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0
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DESeq2 log2FoldChange vs Salmon log2 TPM
R deseq2 salmon rna-seq written 7 months ago by liartom2 • 10 • updated 7 months ago by Antonio R. Franco • 4.2k
4
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0
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306
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0
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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 8 months ago by c_dampier • 60
0
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0
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253
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0
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can't find why certain reads are unmapped by salmon
salmon rna-seq written 8 months ago by vaushev • 10
7
votes
1
answer
595
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1
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Salmon Counts differ in Alignment and Quasi-Mapping mode
alignment salmon rna-seq written 9 months ago by MaxF • 10
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