Question: Xenome Star Aligner
gravatar for lkmklsmn
6.6 years ago by
United States
lkmklsmn930 wrote:

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?


rnaseq • 3.3k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 6.6 years ago by lkmklsmn930

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

ADD REPLYlink written 6.6 years ago by Devon Ryan97k
gravatar for Irsan
6.6 years ago by
Irsan7.2k wrote:

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
ADD COMMENTlink modified 29 days ago by _r_am30k • written 6.6 years ago by Irsan7.2k
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