Questions tagged [salmon]
The salmon tag has no usage guidance.
16 questions
8
votes
1
answer
605
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 ...
7
votes
1
answer
742
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 ...
- 71
6
votes
1
answer
353
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,...
- 2,716
4
votes
0
answers
50
views
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 ...
3
votes
2
answers
346
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 ...
- 364
3
votes
2
answers
369
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 ...
- 15.1k
3
votes
1
answer
185
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 ...
- 719
3
votes
1
answer
78
views
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 ...
- 33
2
votes
1
answer
440
views
Get Salmon mapping/alignment summary
With HISAT2, after the alignment of fastq files you get an alignment summary like this:
...
- 345
2
votes
1
answer
610
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 ...
- 2,578
2
votes
1
answer
55
views
Salmon Multiple File SCRIPT giving error
Hi I am using Salmon quantitation for multiple fastq paired files using following code
...
- 61
1
vote
3
answers
5k
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 ...
- 11
1
vote
1
answer
116
views
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.
...
- 11
1
vote
2
answers
104
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 ...
- 11
0
votes
2
answers
2k
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/...
- 2,578
0
votes
1
answer
681
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:
...
- 2,578