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seq2HLA (version 1.0.0)

Select if your input files are compressed gzipped fastq files:

Leave default (not checked) if you are unsure

Forward FASTQ File:

FASTQ File with forward reads

Reverse FASTQ File:

FASTQ File with reverse reads

Run Name:

Name of the Run

Read Length:

Length of the input reads

Trim x bases from the low quality 3' end:

Trim x bases from the low quality 3' end. Default: 0

Number of threads to use for Bowtie:

Choose a plausible amount of threads to use for Bowtie in this tool

What it does

We developed an in-silico method "seq2HLA", written in python and R, which takes standard paired end RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes, a p-value for each call, and the expression of each class.

Dependencies

bowtie
R

Input

Input files in FASTQ format

Output

Output file(s) in TXT format

Authors

Sebastian Boegel