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wwood / finishm

genome improvement and finishing without further sequencing effort
MIT License
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'roundup' command with paired-end reads #40

Closed minsookim1983 closed 8 years ago

minsookim1983 commented 8 years ago

Hello,

Is it possible to do 'roundup' job with paired-end reads (forward & reverse reads)? In the Usage of 'roundup' job, I could not find any flags for paired-end reads. How about putting in two files one by one? Or, should I merge two reads into a single read? Thank you.

Min-Soo

wwood commented 8 years ago

Hi, Currently FinishM only processes the reads as single-ended. You can put both the forward and reverse in individually and they will be treated as single ended reads. Whether to merge or not depends on your data. If you have high enough coverage then there is probably little point and runs the risk of incorrect overlaps introducing errors, but you might be forced into it if you are only at low coverage.

minsookim1983 commented 8 years ago

I processed 'roundup' job with two paired-end files. However, an error was popped up again. I attached a file containing the error message. roundup.errors.txt It looks about lack of memory in my system. Is it right? Thank you.

Min-Soo

wwood commented 8 years ago

I'm afraid you are correct, you are out of memory. We hope to move away from velvet for this reason in the future, but we aren't there yet. There are various options depending on your situations, the most straightforward of which is to supply finishm less reads.