Questions tagged [salmon]

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3
votes
2answers
47 views

How do I increase the sensitivity of Salmon Alevin?

I'm in a little bit of a bind with targeted single-cell sequencing. I'm trying to match up our reads to the targeted amplicon panel (418 targets), and all but one have matched successfully with Salmon ...
3
votes
2answers
142 views

Calculating most abundant transcript from RNA-Seq data

vcf2maf uses VEP to annotate variants, and I believe selects the default Ensembl transcript to use for annotation. Sometimes the ...
2
votes
1answer
44 views

Get Salmon mapping/alignment summary

With HISAT2, after the alignment of fastq files you get an alignment summary like this: ...
1
vote
2answers
35 views

Bulk RNA-Seq Read Length Normalization across different samples

I have 20 samples out of which 14 are 100 bp in length and 6 are 150 bp. Is there a way to normalize the read length for cross-sample differential expression comparison? What would be the best way to ...
1
vote
3answers
949 views

Download multiple fastq files using fastq-dump

I want to download the following fastq files at the same time in Salmon: - SRR10611214 - SRR10611215 - SRR10611215 - SRR10611216 - SRR10611217 Is there a way ...
7
votes
1answer
614 views

Why are my kallisto and salmon results differing so much just for lncRNA transcripts?

I am running some analysis on an RNA-seq dataset. I have a list of transcripts that are potential lncRNA for which I ran both Kallisto and Salmon aligners. The input data for index building and ...
2
votes
1answer
123 views

RNA-seq analysis of mixed viral/host reads with salmon

I did RNA-seq of mammalian cells infected with pox virus. Now, I have read files which contain both host and virus reads. I want to align the reads both to host and viral genome. I was thinking I ...
4
votes
1answer
459 views

lower mapping rates in salmon v0.13 compared to previous versions

Hi there :) Thanks for the tool! I recently updated to the new salmon (from 0.8... its been a couple years) and I noticed that my mapping percentages change dramatically between the two versions. For ...
2
votes
1answer
366 views

Where to get '--fldMean' and '--fldSD' for single-end Salmon run

I need to run single-end bulk-RNAseq salmon - based alignment and I am not sure what I ...
0
votes
2answers
1k views

tx2gene file for tximport issue

I am trying to use tximport to get raw count matrices of a bulk RNA-seq sequencing experiment. I followed the tutorial: https://bioconductor.org/packages/3.7/bioc/...
6
votes
1answer
230 views

Salmon output: transcripts quantified with zero reads support

I quantified some samples using Salmon. According to the documentation of output format, the last column of the 'Quantification File' represents the number of reads that supported the given transcript,...
0
votes
1answer
407 views

Exception : [Failed to read 8 bytes from input stream! Read 0] salmon quant was invoked improperly

I am trying to run salmon and it keeps giving me 2 java exceptions: ...