Hi,
I’m trying to use the make.sra function to get my 454 reads ready for submission to the SRA.
I’ve produced an oligo file like this:
Forward TCCTGCTAT…
linker TCAG
barcode ACGAGTGCGT 101S
barcode AGCACTGTAG 102S
etc…
And used this oligo to make a mimark template using the get.mimarkspackage function. I’ve then completed the rest of the mimark template, and tried using the make.sra function with the sff file. The function executes properly, and runs for about an hour, but once it’s finished I end up with just four output files:
Output File Names:
Trial_run.fasta
Trial_run.qual
Trial_run.flow
Trial_run.scrap.sff
All of the sff files and sffheader files disappear. The scrap.sff file is very large, and it seems like everything is being put in there, rather than anything being parsed. I can’t figure out what I’m doing wrong - any help would be much appreciated! I can send examples of my oligo and mimarks files, but the sff file is very large.
Thanks