Richard Leggett

I don't know MaSuRCA, but it's not that you need to specify the mate pairs as innies, with a negative std dev, is it?

Hi Patrick, the command looks ok. What did the NextClip screen output look like? Do you still have it? Were there reasonable numbers in each of the categories?

No, sorry, no personal experience. Would be interested to hear how you get on with it.

Hi there, Yes, I would say this is worth doing. However, I wouldn't set the quality threshold too high - use, say, Q20. Thanks, Richard On 1 Jul 2016, at...

Hi there, Yes, it's normal to have paired end and tandem orientation reads in each category. If there is a large percentage, then it's a sign of a bad library....

You're right - NextClip runs without a reference, so doesn't know what orientation reads are in. The pipeline runs on the output files from NextClip, using a reference, so can...

Hi Shigehiro, It sounds like it is, as the error message says, that you've not run nextclip_index_reference.pl (section 5.2 of the manual). This generates a .nextclip file for your reference....

Hi Shigehiro, Many thanks for sending the link. I've passed it on to Matt Clark, one of my co-authors, who is more of a lab person than me! Looks interesting!...