Dear all,

I would like to align some reads to a reference using STAR. The following command works perfectly:

STAR --genomeDir output/spiking/index/star --readFilesIn reads.fastq --outFileNamePrefix outputFolder --runThreadN 8 > message.txt

However, the following command does not work:

STAR --genomeDir output/spiking/index/star --readFilesIn reads.fastq.gz --outFileNamePrefix outputFolder --runThreadN 8 > message.txt

Error: the read ID should start with @ or >

Presumably, STAR expects a FASTQ file and not a fastq.gz file. Does anybody know how to get round this in an efficient way?

Thanks.

C.
add `--readFilesCommand zcat` in your commandline