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Search: Posts Made By: Kristian
Forum: Bioinformatics 04-18-2017, 05:16 AM
Replies: 635
Views: 124,059
Posted By Kristian
Hi Brian, This is Nextera XT prep, and...

Hi Brian,



This is Nextera XT prep, and the adapters/linker were trimmed along with demultplexing directly through Illumina RTA pipeline. On my end the bbduk2 left and right trimming had almost...
Forum: Bioinformatics 04-17-2017, 10:27 AM
Replies: 635
Views: 124,059
Posted By Kristian
Thanks Brian, I sent you a PM with the details....

Thanks Brian, I sent you a PM with the details. I'm using samtools 1.3.1 (and the above is the result of samtools stats
Forum: Bioinformatics 04-17-2017, 04:06 AM
Replies: 635
Views: 124,059
Posted By Kristian
High error rate with BBmap?

Hi Brian,

while trying to call variants on a human MT DNA I noticed the unusually high error rate in mapping with bbmap (37.10 and 36.92 tested) compared to bwa (0.7.12-r1039). Both were run with...
Forum: Bioinformatics 03-27-2017, 09:18 AM
Replies: 93
Views: 18,858
Posted By Kristian
Thanks! What was the issue (to avoid them in the...

Thanks! What was the issue (to avoid them in the future)?
Forum: Bioinformatics 03-25-2017, 07:49 AM
Replies: 93
Views: 18,858
Posted By Kristian
For some reason, two of my posts dod not show up,...

For some reason, two of my posts dod not show up, just a brief answer (to see if it has to do with the attached figures):

1) try pressing f in the main top window, which should give you the list...
Forum: Bioinformatics 03-24-2017, 10:22 AM
Replies: 93
Views: 18,858
Posted By Kristian
Ho-hum, it seems my reply from yesterday never...

Ho-hum, it seems my reply from yesterday never made it to the thread (might be something with the way I linked in the images). Anyway - now I can report more details.

Thanks Brian for the reply!...
Forum: Bioinformatics 03-23-2017, 02:44 PM
Replies: 93
Views: 18,858
Posted By Kristian
on my system (Suse-based) I can add additional...

on my system (Suse-based) I can add additional fields to top by pressing f, then seleccting from a list, and one of them is the nThr, which displays the number of threads. Also, by pressing 'H' in...
Forum: Bioinformatics 03-23-2017, 11:40 AM
Replies: 93
Views: 18,858
Posted By Kristian
Tadpole not honoring threads parameter?

Hi Brian,

I'm trying to run Tadpole through a PBS on a 200-core NUMA machine and I have requested 24 threads for the task. Even though the log file reports Tadpole is using 24 processes, java...
Showing results 1 to 8 of 8

 


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