Question: Hisat2 multiple paired end reads
1
gravatar for sicat.paolo20
14 months ago by
sicat.paolo2030 wrote:

For a single paired end read the script is hisat2 -x /path/to/hg19/indices -1 sample_1.fq.gz -2 sample_2.fq.gz | samtools view -Sbo sample.bam - Our queue is full so I'm not able to test this but is it possible to allign multiple paired end reads in one go and how would I go about it?

hisat2 rna-seq allignment • 978 views
ADD COMMENTlink modified 14 months ago by bioExplorer3.7k • written 14 months ago by sicat.paolo2030
3
gravatar for h.mon
14 months ago by
h.mon24k
Brazil
h.mon24k wrote:

Probably your sample_1.fq.gz and sample_2.fq.gz files already contain multiple reads inside. I guess you want to align multiple files, right?

But do you want the output in a single file, or multiple files as output? For the former, you can pass a comma-separated list of files to hisat2 (see -1 and -2 on hisat2 manual). For the later, there are several option, such as a bash loop, using Parallel, a make script, job arrays (if your queue is managed with SLURM / Torque / SGE), among others options.

ADD COMMENTlink modified 14 months ago • written 14 months ago by h.mon24k

Thank you for the help. I'll be trying to do the latter.

ADD REPLYlink written 14 months ago by sicat.paolo2030
1
gravatar for bioExplorer
14 months ago by
bioExplorer3.7k
bioExplorer3.7k wrote:

If the idea is to run hisat for multiple PE data then this may help:

# Runs of .gz files 
total_files=`find -name '*.gz' | wc -l`
arr=( $(ls *.gz) )

# Alignment

for ((i=0; i<$total_files; i+=2))
{
sample_name=`echo ${arr[$i]} | awk -F "_R1" '{print $1}'`
echo "[Hisat mapping running for sample] $sample_name"
date && time /opt/app/hisat2-2.0.5/hisat2 -p 60 -x $genome_name -1 ${arr[$i]} -2 ${arr[$i+1]} -S $sample_name.sam 
printf "\n\n"
}
ADD COMMENTlink written 14 months ago by bioExplorer3.7k

Thanks for the help. I will look into this.

ADD REPLYlink written 14 months ago by sicat.paolo2030
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1886 users visited in the last hour