salmon

salmon copied to clipboard

Dear salmon support team, I firstly assembled MAGs from my metagenome data, then predicted the ORF gene operons using the prodigal software to generate the corresponding prodigal predicted MAG *faa...

B-1991-ing

Quantification issue: sam file says target has length x but the fasta file contains a sequence of length y

4

I am trying to quantify my reads with salmon quant (v. 1.8.0) and I'm getting an error saying "SAM file says target Vcev1_p0.Chr07.17417.mRNA has length 2346, but the FASTA file...

heeduk

CIGAR in sam file not showing mismatches

3

Hi, I'm looking at RNAseq data and am trying to identify the number of reads that map to an expressed transgene by using salmon in the quantification mapping mode. I...

mej54

When I followed the tutorial here (https://combine-lab.github.io/alevin-tutorial/2020/alevin-features/ ) to perform HTO quantification by alevin (also add --dumpMtx option), a malformed MTX file was generated. Has 999230 nonzero entries, but the...

Xinyue-Lu

Guidance on Minimap2 Settings for Quantification of ONT Reads in Alignment Mode

2

I'm looking for some guidance on recommendations / best practices for quantifying direct RNA / cDNA Nanopore reads using Salmon. It is my understanding that the selective alignment algorithm Salmon...

NanoCoreUSA

Indexing failed, decoy sequences not matching

5

Hello, I tried creating a salmon index for bos taurus but was not successful. I created the decoy file using: grep "^>" decoys.txt sed -i.bak -e 's/>//g' decoys.txt When i...

GiwaAO

Quantification of direct RNA seq reads (ONT) using salmon

4

Hello, Thank you for developing this tool. I am trying to quantify transcript abundance using direct RNA seq reads after mapping with minimap2 to a transcriptome that I got using...

lananh-ngn

Low mapping percentage of reads for non-model organism

3

Hi developers!! ## Background I am using Alevin to align the P.Falciparum single cell dataset. For this sample we got a total of 27% of reads aligning using CellRanger and...

Rohit-Satyam

Salmon modifies the link to the 64-bit x86 C math library

5

**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?** salmon **Describe the bug** I installed Salmon 1.5.2 from binaries, and load it via the module environment...

eboileau

Running alignment mode after hisat + gffread issues

1

Hi all, I have a dataset with 40 samples, which I aligned to a reference transcriptome using HISAT2. I then quantified these using salmon using the alignment mode, with a...

shrhops