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Old 05-12-2014, 05:54 AM   #4
Location: Mountain Grove, MO, USA

Join Date: Apr 2014
Posts: 29

thanks for any and all replies
mastal: if I put -short before the sam, velvet seems to ignore the -reference switch. It then reads both files, puts them together into one file and like I said, I get "read 1" is too long" error.

ctseto: I used both sorted and unsorted files. I used unsorted at first, then noticed that was wrong and then used the very same file(s) that someone else tried for me (and that ran perfectly fine for them) and I ALWAYS get the very same error. Since I want to do an assembly I used the same entire reference seq for velvet that I used for bwa.

I have looked at the alignments (IGV) and yes, there are areas with lots of coverage, and then some without. I am working with a plant, and I do know that there will be lots and lots of repeat elements. but honestly, I do not see how that would stop velvet from even reading my sam file, because the error shows up as soon as the sam file is opening. takes about 3 secs flat .

Any further suggestions anyone?
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