# Salmon¶

Salmon is a tool for transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run Salmon is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your reads. Optinonally, Salmon can make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads.

The read-based mode of Salmon runs in two phases; indexing and quantification. The indexing step is independent of the reads, and only need to be run one for a particular set of reference transcripts. The quantification step, obviously, is specific to the set of RNA-seq reads and is thus run more frequently. For a more complete description of all available options in Salmon, see below.

The alignment-based mode of Salmon does not require indexing. Rather, you can simply provide Salmon with a FASTA file of the transcripts and a SAM/BAM file containing the alignments you wish to use for quantification.

## Using Salmon¶

As mentioned above, there are two “modes” of operation for Salmon. The first, like Sailfish, requires you to build an index for the transcriptome, but then subsequently processes reads directly. The second mode simply requires you to provide a FASTA file of the transcriptome and a .sam or .bam file containing a set of alignments.

Note

Salmon, like eXpress, uses a streaming inference method to perform transcript-level quantification. One of the fundamental assumptions of such inference methods is that observations (i.e. reads or alignments) are made “at random”. This means, for example, that alignments should not be sorted by target or position. If your reads or alignments do not appear in a random order with respect to the target transcripts, please randomize / shuffle them before performing quantification with salmon.

Note

The number of threads that salmon can effectively make use of depends upon the mode in which it is being run. In alignment-based mode, the main bottleneck is in parsing and decompressing the input BAM file. We make use of the Staden IO library for SAM/BAM/CRAM I/O (CRAM is, in theory, supported, but has not been thorougly tested). This means that multiple threads can be effectively used to aid in BAM decompression. However, we find that throwing more than a few threads at file decompression does not result in increased processing speed. Thus, alignment-based salmon will only ever allocate up to 4 threads to file decompression, with the rest being allocated to quantification. If these threads are starved, they will sleep (the quantification threads do not busy wait), but there is a point beyond which allocating more threads will not speed up alignment-based quantification. We find that allocating 8 — 12 threads results in the maximum speed, threads allocated above this limit will likely spend most of their time idle / sleeping.

## Alignment-based mode¶

Say that you’ve prepared your alignments using your favorite aligner and the results are in the file aln.bam, and assume that the sequence of the transcriptome you want to quantify is in the file transcripts.fa. You would run Salmon as follows:

> ./bin/salmon quant -t transcripts.fa -l <LIBTYPE> -a aln.bam -o salmon_quant


The <LIBTYPE> parameter is described below and is shared between both modes of Salmon. After Salmon has finished running, there will be a directory called salmon_quant, that contains a file called quant.sf. This contains the quantification results for the run, and the columns it contains are similar to those of Sailfish (and self-explanatory where they differ).

For the full set of options that can be passed to Salmon in its alignment-based mode, and a description of each, run salmon quant --help-alignment.

Note

Genomic vs. Transcriptomic alignments

Salmon expects that the alignment files provided are with respect to the transcripts given in the corresponding fasta file. That is, salmon expects that the reads have been aligned directly to the transcriptome (like RSEM, eXpress, etc.) rather than to the genome (as does, e.g. Cufflinks). If you have reads that have already been aligned to the genome, there are currently 3 options for converting them for use with Salmon. First, you could convert the SAM/BAM file to a FAST{A/Q} file and then use the read-based mode of salmon described below. Second, given the converted FASTA{A/Q} file, you could re-align these converted reads directly to the transcripts with your favorite aligner and run salmon in alignment-based mode as described above. Third, you could use a tool like sam-xlate to try and convert the genome-coordinate BAM files directly into transcript coordinates. This avoids the necessity of having to re-map the reads. However, we have very limited experience with this tool so far.

Multiple alignment files

If your alignments for the sample you want to quantify appear in multiple .bam/.sam files, then you can simply provide the salmon -a parameter with a (space-separated) list of these files. Salmon will automatically read through these one after the other quantifying transcripts using the alignments contained therein. However, it is currently the case that these separate files must (1) all be of the same library type and (2) all be aligned with respect to the same reference (i.e. the @SQ records in the header sections must be identical).

If you want to use salmon like sailfish, then you first have to build an salmon index for your transcriptome. Again, assume that transcripts.fa contains the set of transcripts you wish to quantify. First, you run the salmon indexer:

> ./bin/salmon index -t transcripts.fa -i transcripts_index


Then, you can quantify any set of reads (say, paired-end reads in files reads1.fa and reads2.fa) directly against this index using the salmon quant command as follows:

> ./bin/salmon quant -i transcripts_index -l <LIBTYPE> -1 reads1.fa -2 reads2.fa -o transcripts_quant


You can, of course, pass a number of options to control things such as the number of threads used or the different cutoffs used for counting reads. Just as with the alignment-based mode, after salmon has finished running, there will be a directory called salmon_quant, that contains a file called quant.sf containing the quantification results.

## What’s this LIBTYPE?¶

Salmon, like sailfish, has the user provide a description of the type of sequencing library from which the reads come, and this contains information about e.g. the relative orientation of paired end reads. However, we’ve replaced the somewhat esoteric description of the library type with a simple set of strings; each of which represents a different type of read library. This new method of specifying the type of read library is being back-ported into Sailfish and will be available in the next release.

The library type string consists of three parts: the relative orientation of the reads, the strandedness of the library, and the directionality of the reads.

The first part of the library string (relative orientation) is only provided if the library is paired-end. The possible options are:

I = inward
O = outward
M = matching


The second part of the read library string specifies whether the protocol is stranded or unstranded; the options are:

S = stranded
U = unstranded


If the protocol is unstranded, then we’re done. The final part of the library string specifies the strand from which the read originates in a strand-specific protocol — it is only provided if the library is stranded (i.e. if the library format string is of the form S). The possible values are:

F = read 1 (or single-end read) comes from the forward strand
R = read 1 (or single-end read) comes from the reverse strand


An example of some library format strings and their interpretations are:

IU (an unstranded paired-end library where the reads face each other)

SF (a stranded single-end protocol where the reads come from the forward strand)

OSR (a stranded paired-end protocol where the reads face away from each other,
read1 comes from reverse strand and read2 comes from the forward strand)


Note

Strand Matching

Above, when it is said that the read “comes from” a strand, we mean that the read should align with / map to that strand. For example, for libraries having the OSR protocol as described above, we expect that read1 maps to the reverse strand, and read2 maps to the forward strand.

For more details on the library type, see Fragment Library Types.

## Output¶

Salmon writes its output in a simple tab-delimited file format. Any line that begins with a # is a comment line, and can be safely ignored. Salmon records the files and options passed to it in comments at the top of its output file. The last comment line gives the names of each of the data columns. The columns appear in the following order:

Each subsequent row described a single quantification record. The columns have the following interpretation.

• Name — This is the name of the target transcript provided in the input transcript database (FASTA file).
• Length — This is the length of the target transcript in nucleotides.
• TPM — This is salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
• FPKM — This is salmon’s estimate of the relative abundance of this transcript in units of Fragments Per Kilobase per Million mapped reads (FPKM). This relative abundance measure is proportional, within-sample, to the TPM measure. However, the TPM should generally be preferred to FPKM. This column is provided mostly for compatibility with tools that expect FPKM as input.
• NumReads — This is salmon’s estimate of the number of reads mapping to each transcript that was quantified. It is an “estimate” insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript. You can round these values to the nearest integer and use them directly as input to count-based methods like Deseq2 and EdgeR, among others.

## Misc¶

Salmon deals with reading from compressed read files in the same way as sailfish — by using process substitution. Say in the read-based salmon example above, the reads were actually in the files reads1.fa.gz and reads2.fa.gz, then you’d run the following command to decompress the reads “on-the-fly”:

> ./bin/salmon quant -i transcripts_index -l <LIBTYPE> -1 <(gzcat reads1.fa.gz) -2 <(gzcat reads2.fa.gz) -o transcripts_quant


and the gzipped files will be decompressed via separate processes and the raw reads will be fed into salmon.

Note

The Mapping Cache

Salmon requires a specific number of observations (fragments) to be observed before it will report its quantification results. If it doesn’t see enough fragments when reading through the read files the first time, it will process the information again (don’t worry; it’s not double counting. The results from the first pass essentially become a “prior” for assigning the proper read counts in subsequent passes).

The first time the file is processed, the set of potential mappings for each fragment is written to a temporary file in an efficient binary format — this file is called the mapping cache. As soon as the required number of obvservations have been seen, salmon stops writing to the mapping cache (ensuring that the file size will not grow too large). However, for experiments with fewer than the required number of observations, the mapping cache is a significant optimization over reading through the raw set of reads multiple times. First, the work of determining the potential mapping locations for a read is only performed once, during the inital pass through the file. Second, since the mapping cache is implemented as a regular file on disk, the information contained within a file can be processed multiple times, even if the file itself is being produced via e.g. process substitution as in the example above.

You can control the required number of observations and thus, indirectly, the maximum size of the mapping cache file, via the -n argument. Note that the cache itself is considered a “temporary” file, and it is removed from disk by salmon before the program terminates. If you are certain that your read library is large enough that you will observe the required number of fragments in the first pass, or if you have some other reason to avoid creating the temporary mapping cache, it can disabled with the --disableMappingCache flag.

Finally, the purpose of making this beta executable (as well as the Salmon code) available is for people to use it and provide feedback. A pre-print and manuscript are in the works, but the earlier we get feedback, thoughts, suggestions and ideas, the better! So, if you have something useful to report or just some interesting ideas or suggestions, please contact us (rob.patro@cs.stonybrook.edu and/or carlk@cs.cmu.edu). Also, please use the same e-mail addresses to contact us with any detailed bug-reports (though bug-support for these early beta versions may be slow).