Closed peterthorpe5 closed 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
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
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