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data61 / gossamer

Gossamer bioinformatics suite
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Xenome classify output file #32

Open ssinghk opened 3 years ago

ssinghk commented 3 years ago

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 commented 2 years ago

Which version are you using? I see this bug in xenome version 1.0.1 downloaded from https://github.com/data61/gossamer/issues/9#issuecomment-402958742

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

dgomezpere commented 2 years ago

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.