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My fastq file of RNA-seq can not be used to estimate HLA classification #9

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lzz-123 opened this issue Jun 7, 2022 · 0 comments

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lzz-123 commented Jun 7, 2022

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?

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