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Forum: Bioinformatics 04-15-2019, 03:17 AM
Replies: 107
Views: 26,521
Posted By Chief_Lazy_Bison
Thank you for the quick advice. I had attempted...

Thank you for the quick advice. I had attempted to merge many samples together at the front end of the pipeline so that I could to all the QC and error correction at once. My problem was fixed when...
Forum: Bioinformatics 04-11-2019, 04:24 AM
Replies: 107
Views: 26,521
Posted By Chief_Lazy_Bison
It is submitted to a SLURM queue via the attached...

It is submitted to a SLURM queue via the attached script.

These reads are a collection of concatenated interleaved paired end libraries

The same script worked well on the individual libraries,...
Forum: Bioinformatics 04-11-2019, 03:01 AM
Replies: 107
Views: 26,521
Posted By Chief_Lazy_Bison
So I resubmitted the job on a node with 40...

So I resubmitted the job on a node with 40 processors and 1TB of memory and I received two very similar exceptions and the job is hanging again.

Exception in thread "Thread-147"...
Forum: Bioinformatics 04-10-2019, 11:07 AM
Replies: 107
Views: 26,521
Posted By Chief_Lazy_Bison
Just resubmitted on a high memory partition,...

Just resubmitted on a high memory partition, hopefully this resolves the issue. Will update once the job finishes.
Forum: Bioinformatics 04-10-2019, 10:03 AM
Replies: 107
Views: 26,521
Posted By Chief_Lazy_Bison
Exclamation java.lang.AssertionError

Hello,

I'm using bbtools to preprocess some metagenomic hiseq reads prior to assembly and I've run into a little issue with clumpify. I am using the recommended 3 step error correction found in...
Forum: Bioinformatics 09-08-2018, 08:46 AM
Replies: 1
Views: 1,226
Posted By Chief_Lazy_Bison
bbmerge detects different adapters

Hello,

I have some bacterial genomes which were sequenced using the Nextera Flex library prep kit ( insert size ~350 bp) and MiSeq paired end reads (2x300). I want to merge these reads with...
Forum: Sample Prep / Library Generation 02-25-2015, 08:15 AM
Replies: 16
Views: 30,498
Posted By Chief_Lazy_Bison
Hello! I recently tried to use some homemade...

Hello!

I recently tried to use some homemade Nextera Index PCR primers (0.5uM final concentration in a limited cycle index PCR reaction). The bioanalyzer results for my first PCR generation...
Forum: Sample Prep / Library Generation 01-19-2015, 08:10 AM
Replies: 1
Views: 1,737
Posted By Chief_Lazy_Bison
Question Nextera indexing and taq polymerases

Hello!

I am trying to sequence (Miseq) a custom amplicon from many samples using the Nextera indexes. For those of you not familiar, this involves a two step PCR protocol. The first round of PCR...
Forum: Sample Prep / Library Generation 12-22-2014, 03:54 PM
Replies: 16
Views: 30,498
Posted By Chief_Lazy_Bison
I found this reply in another thread: ...

I found this reply in another thread:





It seems like there isn't a consensus on this yet, has anyone else had any experience trying to order their own Nextera XT index PCR primers?
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