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Old 05-09-2014, 12:08 PM   #3
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Originally Posted by sfh838t View Post
velveth dir_name 31 -reference ref.fasta -sam illumina_align.sam
If you have single end reads, you should also have '-short' before the '-sam' switch.

Have a look at the Columbus manual.

I would leave the header lines in the sam file.
The sam file should be sorted by read name. The default with samtools is to sort the files by chromosome and alignment position.

Also check the requirements for the reference.fasta file.

Last edited by mastal; 05-09-2014 at 12:15 PM.
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