Xenome classify output file

[ssinghk]

Hello,
I am using xenome classify to process xenograft RNA-seq data. The output species specific .fastq files are missing '@' or '>' and the STAR aligner is unable to map.

[RamRS]

Which version are you using? I see this bug in xenome version 1.0.1 downloaded from #9 (comment)

I use sed '1~4s/^/@/' each_output.fastq to get around it.

[dgomezpere]

Hi,

I would also suggest to introduce a + in the 3rd line of each read with sed -i 's/^$/+/' each_output.fastq.
I found some problems in downstream analyses using the "FASTQ" format from Xenome.