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Old 05-09-2014, 11:35 AM   #2
ctseto
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Location: SE MN

Join Date: Oct 2013
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By its nature, SAM has the alignment in it (SAM=Sequence Alignment Map).

First: Did you sort your SAM file? (will need samtools for this).

Checking the manual again, it looks like it should be:

Code:
velveth $FOLDERNAME $KMER -reference ref.fasta -shortPaired -sam illumina_align.sam
Can you post the first few lines of your sam file by using

Code:
head illumina_align.sam
Since you already have to do the alignment of your reads to the reference, have you tried looking at the alignments? Are there dips in coverage or re-arrangements, things like that?
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