Sailfish quantifies the expression of a given set of transcripts using NGS reads. It is run in two stages: (1) The indexing step is run once per set of transcripts (2) The quantification step is run once for each sample.

References:

• R. Patro, S. M. Mount, and C. Kingsford. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology 2014, 32:462-464. Pubmed |  PMC |  Journal

• GitHub
• Manual

• Module Name: sailfish (see the modules page for more information)
• sailfish is a multithreaded application. Make sure to match the number of cpus requested with the number of threads (-p).
• Example files in SAILFISH_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=8g --cpus-per-task=4 --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ module load sailfish
[user@cn3144]$ zcat $SAILFISH_TEST_DATA/gencode.vM9.transcripts.fa.gz > M9.fa
[user@cn3144]$ sailfish index -t M9.fa -o M9.idx -p $SLURM_CPUS_PER_TASK
[user@cn3144]$ cp $SAILFISH_TEST_DATA/ENCFF138LJO.fastq.gz .
[user@cn3144]$ sailfish quant -i M9.idx -r <(zcat ENCFF138LJO.fastq.gz) --libType U \
                      -o quant -p $SLURM_CPUS_PER_TASK

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. sailfish.sh), which uses the input file 'sailfish.in'. For example:

#! /bin/bash

module load sailfish/0.10.0 || exit 1
wd=$PWD
cd /lscratch/$SLURM_JOB_ID || exit 1

# get transcriptome from the example directory
# This is usually done once - not for each job. Only included
# here to show all steps involved in sailfish quantitation.
zcat $SAILFISH_TEST_DATA/gencode.vM9.transcripts.fa.gz \
    > gencode.vM9.transcripts.fa

# index the transcripts
sailfish index -t gencode.vM9.transcripts.fa -o gencode.vM9.idx \
    -p $SLURM_CPUS_PER_TASK

# quantify the transcripts
cp $SAILFISH_TEST_DATA/ENCFF138LJO.fastq.gz .
sailfish quant -i gencode.vM9.idx -l U \
    -r <(zcat ENCFF138LJO.fastq.gz) \
    -o quant -p $SLURM_CPUS_PER_TASK
cp -r quant $wd

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=8g --gres=lscratch:16 sailfish.sh

Create a swarmfile (e.g. sailfish.swarm). For example:

sailfish quant -i gencode.vM9.idx -l U -r <(zcat sample1.fq.gz) \
    -o quant_sample1 -p $SLURM_CPUS_PER_TASK
sailfish quant -i gencode.vM9.idx -l U -r <(zcat sample2.fq.gz) \
    -o quant_sample2 -p $SLURM_CPUS_PER_TASK
sailfish quant -i gencode.vM9.idx -l U -r <(zcat sample3.fq.gz) \
    -o quant_sample3 -p $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f sailfish.swarm -g 8 -t 8 --module sailfish/0.10.0