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TRON-Bioinformatics / seq2HLA

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard 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 (in 4 digit resolution), a p-value for each call, and the expression of each class.
MIT License
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ClassI-class-2nditeration_1.fq empty #4

Closed peterthorpe5 closed 3 years ago

peterthorpe5 commented 4 years ago

Dear seq2HLA,

I installed the requisites through conda, however, when I try to run this is always stops after the first iteration. Therefore, ClassI-class-2nditeration_1.fq is always empty. This is the same for ~20 cell lines. (RNAseq fq input).

An example bowtie log is:

reads processed: 8494272

reads with at least one reported alignment: 660 (0.01%)

reads that failed to align: 8493612 (99.99%)

Reported 49859 paired-end alignments to 1 output stream(s)

bowtie version 1.1.2

please could you point me in the direction of a fix?

REgards,

Peter Thorpe

sebboegel commented 3 years ago

Dear Peter,

sorry for the late reply. Is the issue still an issue? How does the HLA class I typing text file looks like?

Best,

Sebastian

peterthorpe5 commented 3 years ago

Hi Sebastian,

Thank you very much for your reply. I am sorry this project has finished now for me .... I cannot replicate the work without getting access to the data again.

cheers,

Pete