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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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Add '/1' to headers of single-end fastq files for compatibility with Trinity #54

Closed idalind closed 6 years ago

idalind commented 6 years ago

Trinity fails in single-end mode unless the fastq headers end with '/1' or '/2'. TraCeR now adds '/1' at the end of each fastq header if run in single-end mode.

idalind commented 6 years ago

Sorry Mike, I was being unclear. I don't think that will ever happen. What the code does is add "/1" to the fastq file TraCeR creates when splitting the SAM file for input to Trinity. Then TraCeR adds "/1" or "/2" according to the mate flag for paired-end reads, but currently doesn't add "/1" or "/2" for single-end reads. Trinity was complaining about this.