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.
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My fastq file of RNA-seq can not be used to estimate HLA classification #9
when I use seq2HLA, some errors occurred as follow:
First iteration starts....
Mapping ......
reads processed: 102029138
reads with at least one reported alignment: 0 (0.00%)
reads that failed to align: 102029138 (100.00%)
No alignments
Calculation of first digital haplotype.....
The digital haplotype is written into test-ClassI-nonclass.digitalhaplotype1
1st iteration done.
Now removing reads that mapped to the three top-scoring groups .......
Nothing to remove
Second iterations starts .....
Mapping ......
Error: reads file does not look like a FASTQ file
I have no idea why my fastq file of RNA-seq cannot be used. Any recommendations to solve my problems?
when I use seq2HLA, some errors occurred as follow: First iteration starts.... Mapping ......
reads processed: 102029138
reads with at least one reported alignment: 0 (0.00%)
reads that failed to align: 102029138 (100.00%)
No alignments
Calculation of first digital haplotype..... The digital haplotype is written into test-ClassI-nonclass.digitalhaplotype1 1st iteration done. Now removing reads that mapped to the three top-scoring groups ....... Nothing to remove
Second iterations starts ..... Mapping ...... Error: reads file does not look like a FASTQ file
I have no idea why my fastq file of RNA-seq cannot be used. Any recommendations to solve my problems?