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Counting Ribo-seq data on gene and transcript level?
riboseq salmon featurecounts rna-seq written 10 days ago by BPors • 40
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5 follow
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salmon NumReads inconsistent with depth from --writeMappings?
software error R salmon samtools rna-seq written 15 days ago by ningyuan.sg • 0
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Is there Quality score/measure to compare salmon results using different kmer values?
salmon rna-seq written 11 days ago by karni_bedirian • 0 • updated 11 days ago by ATpoint ♦ 19k
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Does salmon use phred scores while pseudoaligning (and/or validating mapping)?
salmon phred written 10 weeks ago by Anthony • 0 • updated 11 days ago by karni_bedirian • 0
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Comparing different transcripts expression level of a list of genes from one condition
R deseq2 salmon kallisto rna-seq written 11 days ago by mr.monahton • 20 • updated 11 days ago by andrew.j.skelton73 ♦ 5.8k
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Use Salmon to annotate a Sam file
alignment quantification salmon rna-seq written 16 days ago by Florian Bernard • 50 • updated 16 days ago by ATpoint ♦ 19k
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Where can I download the Danio Rerio (zebrafish) transcriptome?
zebrafish salmon rna-seq genomics transcriptome written 4 weeks ago by dtatarak • 10 • updated 17 days ago by Biostar ♦♦ 20
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Which bias flags to run with Salmon before DESeq2 analysis?
deseq2 salmon bias flags rna-seq written 23 days ago by cameron.holman • 0
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138
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Salmon quasi Index upgrade
salmon rna-seq written 6 weeks ago by Morris_Chair • 120 • updated 6 weeks ago by RamRS ♦ 22k
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187
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How to build a transcriptome reference ?
salmon rna-seq written 6 weeks ago by darbinator • 190
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273
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Ensembl gene annotation GRCh37.87
ensembl salmon rna-seq written 3 months ago by F • 3.4k • updated 3 months ago by genomax ♦ 69k
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283
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DESeq2 log2FoldChange vs Salmon log2 TPM
R deseq2 salmon rna-seq written 3 months ago by liartom2 • 10 • updated 3 months ago by Antonio R. Franco • 4.1k
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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 4 months ago by c_dampier • 50
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can't find why certain reads are unmapped by salmon
salmon rna-seq written 4 months ago by vaushev • 10
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Salmon Counts differ in Alignment and Quasi-Mapping mode
alignment salmon rna-seq written 5 months ago by MaxF • 10
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Highly uneven RINs, mapping rates, and methods to deal with this (normalisation, salmon)
salmon rna-seq normalisation written 5 months ago by chris86 • 290
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Salmon: Any downstream DEA tools which uses abundance estimate variation information?
deseq2 salmon written 5 months ago by Thomas Bradley • 90
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What transcript quantification tool would you recommend for 3' prime RNA-seq?
transcript quantification salmon rna-seq written 6 months ago by roy.granit • 800 • updated 6 months ago by WouterDeCoster ♦ 40k
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how do normalization for transcript length
tximport transcript coverage salmon plot written 6 months ago by lkianmehr • 30
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195
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Hypsibius dujardini locus ID conversion
alignment salmon rna-seq written 7 months ago by stanley.ju • 0
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FASTQ alignment result is really bad
htseq-count salmon rna-seq written 7 months ago by bharata1803 • 420 • updated 7 months ago by h.mon ♦ 26k
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repeatmask fasta file
teelements salmon repeatmask index written 8 months ago by lkianmehr • 30 • updated 8 months ago by Biostar ♦♦ 20
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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 2.5 years ago by james.lloyd • 80 • updated 8 months ago by lalvarez • 10
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May I use numreads for doing DGE after quantifying by Salmon
salmon dge written 8 months ago by lkianmehr • 30 • updated 8 months ago by WouterDeCoster ♦ 40k
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salmon - tximport - deseq2 gene level workflow
tximport deseq2 salmon rna-seq written 8 months ago by jomo018 • 480
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rRNA removal needed for salmon / DESeq2 analysis
rrna deseq2 salmon contamination written 8 months ago by mark.dunning • 200
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Bash: salmon command not found
salmon rna-seq bash written 8 months ago by ab123 • 40
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Average Insert Size When Using Transcript Quantification Tools Such as Salmon?
next-gen salmon rna-seq written 8 months ago by Dru Zod • 0 • updated 8 months ago by Rob ♦ 3.4k
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Alignment-free tools (like Kallisto or Salmon): useful for bacterial transcriptomes?
bacteria salmon rna-seq written 8 months ago by arctan • 0 • updated 8 months ago by Istvan Albert ♦♦ 80k
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Orientation of reads in .fastq files from RNA-Seq
salmon rna-seq written 9 months ago by newbio17 • 10 • updated 9 months ago by swbarnes2 ♦ 6.0k
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