Xenome Star Aligner

Question

[lkmklsmn]

Hi,
after having classified reads from xenograft experiment using xenome. I try aligning human reads using STAR aligner.
Pseudo code looks like this: STAR --genomeDir genome --readFilesIn human_1.fastq human_2.fastq
Then I get the error:

EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >

Apr 11 12:13:31 ...... FATAL ERROR, exiting [samopen] SAM header is present: 25 sequences. [sam_read1] reference 'SN:chrM LN:16571 66

What does this error mean? Are the human_*.fastq xenome outputs in a format unrecognizable by STAR?

Thanks

[Devon Ryan]

Can you post the first few (10 or so) lines of each of the fastq files?

Answer 1

[Irsan]

yup, you just need to add the @ character at the beginning of each seq id in your classified fastq.

cat human_1.fastq | paste - - - - | sed 's/^/@/g' | sed 's/\t/\n/g' > human_repaired1.fastq