Shulou(Shulou.com)06/02 Report--

This article will explain in detail how to use RNA-seq data for HLA typing in HLAforest. The content of the article is of high quality, so the editor will share it with you for reference. I hope you will have a certain understanding of the relevant knowledge after reading this article.

1. Modify config.sh

The main purpose is to modify the options HLAFOREST_HOME and NUM_THREADS. Examples are as follows

#! / bin/bash# User modifiable variablesHLAFOREST_HOME=/soft/hlaforest/NUM_THREADS=10 # the number of threads bowtie should use

HLAFOREST_HOME specifies the installation directory of the software, and NUM_THREADS specifies the number of threads compared by bowtie.

two。 Modify CallSimulation.sh

Adjust the settings of CONFIG_PATH

CONFIG_PATH=/soft/hlaforest/scripts/config.sh3. Modify CallHaplotypesPE.sh

Adjust the settings of CONFIG_PATH

CONFIG_PATH=/soft/hlaforest/scripts/config.sh4. Add PATH environment variable

In the configuration file of the environment variable, add the scripts directory to the PATH variable to make it easier for the program to call, as follows

Export PATH=/soft/hlaforest/scripts:$PATH

After the above parameters have been adjusted, the software can be run. It should be noted that the software relies on bioperl and bowtie, and since my system has already been installed, the installation process of these two software is not given here.

The software comes with its own test data set, which can be used as follows

CallHaplotypesPE.sh test2/ test2/gm12878_short_1.fastq test2/gm12878_short_2.fastq

You only need to specify the original file that is sequenced at both ends. The default typing result is saved in haplotypes.txt. The contents of this file are shown below.

ROOT:A ROOT:A:11 ROOT:A:11:01 ROOT:A:11:01:04ROOT:A ROOT:A:01 ROOT:A:01:01 ROOT:A:01:01:01 ROOT:A:01:01:01:01ROOT:B ROOT:B:55 ROOT:B:55:01 ROOT:B:55:01:01ROOT:B ROOT:B:08 ROOT:B:08:01 ROOT:B:08:01:01 is related to HLAforest and how to use RNA-seq data for HLA typing is shared here. I hope the above content can be of some help to you and learn more knowledge. If you think the article is good, you can share it for more people to see.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.