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Questions tagged [salmon]

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Salmon Multiple File SCRIPT giving error

Hi I am using Salmon quantitation for multiple fastq paired files using following code ...
Malik Saad's user avatar
1 vote
1 answer

After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?

I have been running nf-core in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA ...
user18959's user avatar
4 votes
0 answers

Salmon Pseudo count when dealing with male and female RNA-seq data

I've generated a quant seq data that I intend to use to compare male and female gene expresion, with a focus on sexual chromosome. For my species (three-spined stickleback), it is a classic XY sex ...
Florent Sylvestre's user avatar
1 vote
1 answer

Snakemake MissingRuleException

I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message. ...
Hua Yuan's user avatar
2 votes
2 answers

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 ...
gringer's user avatar
  • 14.1k
3 votes
2 answers

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 ...
Tomas Bencomo's user avatar
2 votes
1 answer

Get Salmon mapping/alignment summary

With HISAT2, after the alignment of fastq files you get an alignment summary like this: ...
justinian482's user avatar
1 vote
2 answers

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 ...
so_close_yet's user avatar
1 vote
3 answers

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 ...
Lily's user avatar
  • 11
7 votes
1 answer

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 ...
Marta Silva's user avatar
3 votes
1 answer

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 ...
L R Joshi's user avatar
  • 719
8 votes
1 answer

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 ...
Courtney Stairs's user avatar
2 votes
1 answer

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 ...
Nikita Vlasenko's user avatar
0 votes
2 answers

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:
Nikita Vlasenko's user avatar
6 votes
1 answer

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,...
aechchiki's user avatar
  • 2,676
0 votes
1 answer

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: ...
Nikita Vlasenko's user avatar