Double Digtest Rad-Seq (Ddrad)
Does anyone have experience running the ddRAD pipeline of Peterson et al? I'm running on a MiSeq run of data and the amount of disk space it seems to require is huge. I modified one of the files so that it deletes BLAT files, which helps, but the intermediate *.label files, which will be required for the MCL step, are also approaching a few hundred MB to close to a GB each per query (I have the sequences split in to 4000 query files).
I could try reducing the number of individuals from the samples, which may be my only option.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Pipeline for phasiRNA detection
written by v.baaskarla •
-
quality filtering of Miseq dataset
written by User 4014 •
-
fast global amino acid alignment without db creation
written by Leszek
-
Where To Find Encode Dnase I Footprint Data
written by joshualevipayne
-
Samtools Pipelines
written by Geparada
-
Macs 1.4 Reports Many Negative P-Values
written by Konrad Rudolph •
-
Parallel Bzip2 In Abyss
written by ALchEmiXt
-
Pipeline To Map 60-Mers To Genes
written by David Quigley
-
Question About Transfac Database Data Quality
written by Zhe Liu •
-
What Is The Best Method For Aligning Two Genome Assemblies?
written by Aaronquinlan
Hi,Dan. Maybe you can run it with --cleanup method!
I did, the problem is that the the files in question are necessary at the next step, after which cleanup would be invoked. I also had to go in and manually set a flag to not keep the Blat files in the code. It is a boolean option hardcoded as TRUE with checks in the code for what to do if it is false, but the flag can;t be set by an external option.