Shulou(Shulou.com)06/01 Report--

This article introduces how seq2 HLA uses RNA_seq data for HLA typing. The content is very detailed. Interested partners can refer to it for reference. I hope it can help everyone.

For different HLA Allels, the differences between exon2 and exon3 sequences are particularly obvious, and many HLA typing software will sort out HLA Allel sequence reference databases according to this part of sequence.

seq2HLA also adopts a similar strategy. Through the sequences of exon2 and exon3 of HLA different Allels, an HLA reference database is collated. By comparing the reads of RNA_seq with this database, HLA typing results are determined. The principle diagram is as follows.

Iterative twice, each time picking out the highest coverage of the Allil as the typing results.

seq2HLA is developed in Python and R. The installation process is relatively simple. Download the source code directly. The installation process is as follows.

git clone https://github.com/TRON-Bioinformatics/seq2HLAcd seq2HLA/

The usage is as follows:

python seq2HLA.py -1 R1.fastq -2 R2.fastq -r test -p 10

The-1 and-2 arguments specify the fastq format sequence on the input R1 and R2 sides, respectively; the-r argument specifies the prefix of the output file name, and-p specifies the number of threads, mainly the threads in bowtie alignment.

There are many output files, the detailed list is as follows

test.ambiguitytest-ClassI-class.bowtielogtest-ClassI-class.expressiontest-ClassI-class.HLAgenotype2digitstest-ClassI-class.HLAgenotype4digitstest-ClassII.bowtielogtest-ClassII.expressiontest-ClassII.HLAgenotype2digitstest-ClassII.HLAgenotype4digitstest-ClassI-nonclass.bowtielogtest-ClassI-nonclass.expressiontest-ClassI-nonclass.HLAgenotype2digitstest-ClassI-nonclass.HLAgenotype4digits

We mainly focus on the result file with the suffix HLA genotype 4digits. As you can see, the typing results of HLA Clas I and Class II genes are used simultaneously. Take the HLA I gene 4-site typing results as an example, the file contents are as follows

#Locus Allele 1 Confidence Allele 2 ConfidenceA A*02:65 0.008687167 A*02:65 NAB B*39:05' 0.3821314 B*13:48 0.09848174C C*08:02' NA C*08:02 NA

For HlA genotype I, the typing results of A, B and C genes are given, and each gene is given two allels. For each Allel, the corresponding score value will be given.

About seq2HLA how to use RNA_seq data for HLA typing is shared here, I hope the above content can be of some help to everyone, you can learn more knowledge. If you think the article is good, you can share it so that more people can see it.

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.