Maximum sequence length

[Lisle Mose]

Hello,

Is there a maximum input sequence length that STAR can handle?  I'm attempting to align assembled contigs (of varying length), but I get the following error message in stderr:

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

Oct 10 10:45:10 ...... FATAL ERROR, exiting

If I filter contigs of length 10k or greater, the error goes away.  I've compiled using make STARlong.  Is there a way to map these longer contigs using STAR?

Thanks,

Lisle

[Alexander Dobin]

Hi Lisle,

when compiled as STARlong, STAR should be able to handle sequences up to 50kb.

STAR can handle "multi-line" (i.e. sequence split in multiple lines) FASTA, but not FASTQ.

Please send me a small portion of your file for which you can still see the error.

Cheers

Alex