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Search: Posts Made By: jpummil
Forum: Bioinformatics 10-03-2019, 09:09 AM
Replies: 3
Views: 1,024
Posted By jpummil
Haha! Well, THAT didn't work! BWA did OK with the...

Haha! Well, THAT didn't work! BWA did OK with the indexing, etc...but Pilon quickly bailed:

Suppressed: java.lang.IllegalStateException: Inappropriate call if not paired read

I'll go back and...
Forum: Bioinformatics 10-02-2019, 06:23 AM
Replies: 3
Views: 1,024
Posted By jpummil
Kind of leaning that way for sure. I dug around a...

Kind of leaning that way for sure. I dug around a bit in the MaSuRCA documentation and have identified and located the "corrected" PE data created during assembly:

pe.cor.fa - error corrected PE...
Forum: Bioinformatics 09-30-2019, 11:29 AM
Replies: 3
Views: 1,024
Posted By jpummil
Using Pilon after MaSuRCA Assembly

So, lots of good threads on using Pilon...but my question is specifically about the use of Pilon after using MaSuRCA for assembly. MaSuRCA specifically states that the unmodified, raw reads be used...
Forum: Oxford Nanopore 10-24-2017, 09:11 AM
Replies: 1
Views: 4,050
Posted By jpummil
MinION Computer Requirements

So, one of our Bio Lab groups just received their first MinION sequencer and there has been a bit of debate as to selection of computer to support the device. The latest ONT reference document says...
Forum: Bioinformatics 04-18-2017, 01:26 PM
Replies: 2
Views: 1,543
Posted By jpummil
So, last time this was discussed on SeqAnswers...

So, last time this was discussed on SeqAnswers appears to have been mid-2016, and the answers were as I would expect:
http://seqanswers.com/forums/showthread.php?t=69742&highlight=GPU

After a lot...
Forum: Bioinformatics 04-17-2017, 11:06 AM
Replies: 2
Views: 1,543
Posted By jpummil
GPU Enabled Bioinformatics Applications

In a bit of a debate with a colleague about how many (or, as I put it, how FEW) application codes are currently GPU-enabled in the wide application case considered "Bioinformatics". Of course, it...
Forum: Bioinformatics 03-13-2017, 11:43 AM
Replies: 5
Views: 1,814
Posted By jpummil
Ashlee, Can you post the command that...

Ashlee,

Can you post the command that specifies 0.03?

I wonder if the 0.03 requires a unique processing step back a few more commands to appropriately set your data correctly for the 0.03 you...
Forum: Pacific Biosciences 01-21-2017, 05:57 PM
Replies: 17
Views: 9,422
Posted By jpummil
Apologies, attached is Quast report comparing...

Apologies, attached is Quast report comparing base Canu assembly, Base + Quiver polishing, and Quiver + Pilon....

Note, still using --glimmer for gene finding in Quast. Need to switch over to...
Forum: Pacific Biosciences 01-20-2017, 07:02 AM
Replies: 17
Views: 9,422
Posted By jpummil
Results of using Pilon AFTER having used...

Results of using Pilon AFTER having used Quiver....

So, Pilon just completed after 40+ hours of computation....another small increase in file size from what Quiver provided...

-rw-rw-r-- 1...
Forum: Pacific Biosciences 01-18-2017, 06:08 AM
Replies: 17
Views: 9,422
Posted By jpummil
So, I still need to write up a brief process...

So, I still need to write up a brief process workflow to describe what I've doe thus far, but thought I'd update anyone following this thread on another step I heard about thru the grapevine (people...
Forum: Pacific Biosciences 12-21-2016, 08:15 AM
Replies: 17
Views: 9,422
Posted By jpummil
SUCCESS! Not a huge improvement on the...

SUCCESS!

Not a huge improvement on the original assembly (using Canu)...but improved gene's found using Quast (comparison attached).

I used default parameters in Quiver, not sure tweaking...
Forum: Pacific Biosciences 12-20-2016, 10:43 AM
Replies: 17
Views: 9,422
Posted By jpummil
Thanks gconcepcion! That definitely did the...

Thanks gconcepcion! That definitely did the trick. Ran into a /tmp space issue next. THINK I have it solved by supplying the --tmpDir option in the command line and setting it to the /local_scratch...
Forum: Pacific Biosciences 12-19-2016, 03:09 PM
Replies: 17
Views: 9,422
Posted By jpummil
Used bax2bam to convert all of the bax.h5 files...

Used bax2bam to convert all of the bax.h5 files to .bam format...no problem.

When I try to use pbalign on the 10ea .bam files, it complains after it appears to read and accept the first three...
Forum: Pacific Biosciences 12-16-2016, 09:57 AM
Replies: 17
Views: 9,422
Posted By jpummil
Thanks rhall! Was just about to post an update...

Thanks rhall! Was just about to post an update when you posted this ;-)

-rw-r--r-- 1 jpummil jpummil 2.3G Dec 16 12:06 m160611_230902_00125_c101003722550000001823226809161614_s1_p0.1.bax.h5
...
Forum: Pacific Biosciences 12-15-2016, 04:39 PM
Replies: 17
Views: 9,422
Posted By jpummil
Hmmm...apparently some misunderstanding about...

Hmmm...apparently some misunderstanding about "movies" on my part.

Using the following bax2bam command:
bax2bam Q1133.bax.h5/*.bax.h5 -o movie --subread


ERROR: multiple movies detected:...
Forum: Pacific Biosciences 12-14-2016, 09:49 AM
Replies: 17
Views: 9,422
Posted By jpummil
Genome size is about 170Mb....and I have ~65GB of...

Genome size is about 170Mb....and I have ~65GB of bax.h5 files. BUT...I also have a pretty robust linux server to run it on.
Forum: Pacific Biosciences 12-14-2016, 09:43 AM
Replies: 17
Views: 9,422
Posted By jpummil
Thanks so much, rhall! Just getting my data set...

Thanks so much, rhall! Just getting my data set up for a trial now ;-)

I'll update the thread when I'm done!
Forum: Pacific Biosciences 12-13-2016, 06:40 PM
Replies: 17
Views: 9,422
Posted By jpummil
Blasr/Quiver - Best Practice for Current Versions?

So, first time attempting to use quiver to polish an assembly I created in Canu. All of the software is installed and functional via command line (quiver, pbalign, bax2bam, quiver, arrow, etc). Our...
Forum: Bioinformatics 10-06-2016, 09:44 AM
Replies: 8
Views: 4,030
Posted By jpummil
The assembly itself using miniasm and the...

The assembly itself using miniasm and the conversion script from gfa to fasta worked fine, though the assembly isn't as "good" as from Canu.

Still no really good way to estimate a genome size from...
Forum: Bioinformatics 09-28-2016, 09:01 AM
Replies: 1
Views: 1,420
Posted By jpummil
Canu sensitivity to genomeSize parameter

I am currently working with some Bio faculty on a de novo assembly of Centruroides vittatus (Striped Bark Scorpion). One difficulty I seem to be having involves the command line parameter...
Forum: Bioinformatics 07-15-2016, 06:51 AM
Replies: 8
Views: 4,030
Posted By jpummil
Thanks for the suggestion wdecoster ;) I think...

Thanks for the suggestion wdecoster ;) I think I've avoided miniasm thus far because it appears to only output .gfa files? Kind of limits further evaluation of the assembly as most common tools seem...
Forum: Bioinformatics 07-14-2016, 06:48 PM
Replies: 8
Views: 4,030
Posted By jpummil
Thanks for the quick response, Brian! Good...

Thanks for the quick response, Brian!

Good to know about the comma-delimited method for multiple entries. Unfortunate to hear about the PacBio error issue when trying to determine genome size. I...
Forum: Bioinformatics 07-14-2016, 11:35 AM
Replies: 8
Views: 4,030
Posted By jpummil
Genome Size Estimation from PacBio Raw Reads

So, working on a de novo assembly using Canu, and it seems to be VERY sensitive to the genomeSize=XXX parameter which is required. As it is a new project, no one has an actual "size" on it (checked T...
Forum: Bioinformatics 04-24-2015, 07:04 AM
Replies: 3
Views: 2,687
Posted By jpummil
I wonder if we should have a "sticky" for this...

I wonder if we should have a "sticky" for this topic as it comes up quite bit. We'd never get complete consensus among the community, but some solid guidelines look to be needed by many. Sort of an...
Forum: Bioinformatics 04-14-2015, 07:30 AM
Replies: 252
Views: 104,265
Posted By jpummil
I've never resolved this issue either. Really...

I've never resolved this issue either. Really need to use the tool, but haven't been able to circumvent the error issue with -x 1
Showing results 1 to 25 of 85

 


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