SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 88
Search took 0.01 seconds.
Search: Posts Made By: jnfass
Forum: Pacific Biosciences 12-09-2014, 10:27 AM
Replies: 12
Views: 6,423
Posted By jnfass
@rhall Interesting ... I haven't seen this...

@rhall Interesting ... I haven't seen this smrtmake stuff before. I'd note that the default OVLSIZE (20000) for circularize.mk seems large; I'm looking at two circular bacterial genomes (~5Mbp size)...
Forum: Pacific Biosciences 12-05-2014, 08:49 AM
Replies: 12
Views: 6,423
Posted By jnfass
@EulnayM I see the same thing with Gepard and...

@EulnayM I see the same thing with Gepard and sprai's check_circularity.pl script. Gepard shows clear ~6kbp overlap (after zooming in on the 5'-end to 3'-end region of the dot plot) with ~100%...
Forum: Pacific Biosciences 03-18-2013, 01:40 PM
Replies: 17
Views: 12,377
Posted By jnfass
Modified CommandRunner.py worked; what exactly did it do?

This change allowed me to complete a PBJelly run; thanks! I made a copy of the original CommandRunner.py script, as well as a modified copy. Copied the modified version (with 2 minute timeout) over...
Forum: Bioinformatics 12-20-2012, 03:14 PM
Replies: 1
Views: 1,780
Posted By jnfass
Are you sure the plot is different for aligned...

Are you sure the plot is different for aligned sequence? Wherever you're looking, if you left-click on a location in one or the other sequence, the other sequence(s) will shift to line up with the...
Forum: Genomic Resequencing 05-18-2012, 12:25 AM
Replies: 3
Views: 4,861
Posted By jnfass
randomly came across this - kinda sad that you've...

randomly came across this - kinda sad that you've had no answers - doesn't bode well for the community.

In any case, could this have been coming from contaminated "mate-pair" libraries (from large...
Forum: Bioinformatics 05-07-2012, 12:44 PM
Replies: 4
Views: 2,974
Posted By jnfass
I should have mentioned that I found my issue. I...

I should have mentioned that I found my issue. I was careless before in saying that all my spliced alignments had XS:A:[+-] tags. Some of them instead have XS:A:? tags (presumably where the...
Forum: Bioinformatics 05-02-2012, 03:25 AM
Replies: 4
Views: 2,974
Posted By jnfass
I'll third this complaint ... with SAM generated...

I'll third this complaint ... with SAM generated by GMAP. I've checked, and all of the records with N's in CIGAR strings do have XS:A:[+-] tags. I had wondered if there was a specific order that...
Forum: Bioinformatics 04-11-2012, 01:05 PM
Replies: 26
Views: 10,697
Posted By jnfass
Thanks for writing and making samscope available....

Thanks for writing and making samscope available. I struggled for a little bit with building it myself, and ran into mchaisso's problem (maybe?) where it seemed that the boost libraries weren't being...
Forum: RNA Sequencing 04-10-2012, 12:52 PM
Replies: 7
Views: 3,916
Posted By jnfass
If you're comfortable working on the command line...

If you're comfortable working on the command line (linux/unix, Mac OS X terminal?) and have samtools installed, use 'samtools view' ...
If not, can you get helpful details about the aligned reads by...
Forum: Bioinformatics 04-10-2012, 12:19 PM
Replies: 5
Views: 4,579
Posted By jnfass
I'm having trouble finding bioinformatics...

I'm having trouble finding bioinformatics protocols for doing this too. The problem seems to be that most tools (scripture, PASA?, IsoInfer, Inchworm, IsoEM, NSMAP, MISO are most of what I've looked...
Forum: RNA Sequencing 04-10-2012, 12:11 PM
Replies: 7
Views: 3,916
Posted By jnfass
Are there different read groups, perhaps two...

Are there different read groups, perhaps two different samples in the BAM? How was it produced (tool, command example, etc.)? Maybe you could show examples of SAM lines from each of the two files ...
Forum: 454 Pyrosequencing 01-23-2012, 02:57 PM
Replies: 6
Views: 4,470
Posted By jnfass
Can I ask, biocomfun, how you used CORAL to...

Can I ask, biocomfun, how you used CORAL to correct 454 reads using Illumina reads? As far as I can tell, CORAL simply takes a set of reads and does multiple alignment ... i.e. you can't specify a...
Forum: Bioinformatics 12-02-2011, 09:48 AM
Replies: 9
Views: 6,070
Posted By jnfass
@slowsmile - can you comment on the p-values /...

@slowsmile - can you comment on the p-values / fold changes, especially in light of @Jon_Keats' post? Do the stats for the original 173 genes (presumably the most obvious DE cases) remain roughly the...
Forum: Bioinformatics 08-05-2011, 11:32 AM
Replies: 6
Views: 12,754
Posted By jnfass
Yes, on both counts. By the way, the...

Yes, on both counts.

By the way, the -exp_cov value is used to determine which parts of the graph are likely due to repeat sequence ... some multiple (maybe 1.5?? I forget...) of the -exp_cov...
Forum: Bioinformatics 07-20-2011, 10:40 AM
Replies: 1
Views: 2,335
Posted By jnfass
Hey John! I'm looking for this as well ... did...

Hey John! I'm looking for this as well ... did you ever get an answer from somewhere else? Specifically I think I'm seeing reduced (compared to alignments using bwa-0.5.8?) mapping qualities for...
Forum: Bioinformatics 06-20-2011, 01:56 PM
Replies: 292
Views: 161,804
Posted By jnfass
@oudacontrol: You should post the command you...

@oudacontrol: You should post the command you used. It seems like the command may have been mis-formatted, but there's no way to tell if you don't include it.
Forum: Bioinformatics 05-19-2011, 10:03 AM
Replies: 13
Views: 10,239
Posted By jnfass
Library type / depth issues

Some of the parameters of the data (library insert sizes, depths) are determined more by the parties who are willing to donate novel data "to the cause," rather than pure ab initio considerations of...
Forum: Bioinformatics 05-18-2011, 10:02 AM
Replies: 13
Views: 10,239
Posted By jnfass
Linked to Genome10K Project

Hi all,

This was actually a collaborative effort between David Haussler's group at UCSC, Ian Korf's lab here at UC Davis, and the UC Davis Genome Center's Bioinformatics Core. David Haussler...
Forum: Bioinformatics 05-11-2011, 12:41 PM
Replies: 19
Views: 142,356
Posted By jnfass
I think there's some diversity in the literature,...

I think there's some diversity in the literature, but I wouldn't claim to have seen all of the places its definition is discussed. The wikipedia article's 1st and 2nd paragraph are inconsistent, it...
Forum: Bioinformatics 03-09-2011, 12:05 PM
Replies: 31
Views: 19,002
Posted By jnfass
Ok ... thanks. You're probably referring to...

Ok ... thanks.

You're probably referring to this (http://www.openbioinformatics.org/annovar/annovar_faq.html#othergenome).
Forum: Bioinformatics 03-09-2011, 11:37 AM
Replies: 31
Views: 19,002
Posted By jnfass
@Michael.James.Clark ... Annovar seems to require...

@Michael.James.Clark ... Annovar seems to require annotation databases from the UCSC Genome Browser. That doesn't exist for at least part of the genome I'm working with.

@nexgengirl ... Polyphen-2...
Forum: Bioinformatics 03-03-2011, 01:45 PM
Replies: 31
Views: 19,002
Posted By jnfass
Thanks, but it seems to only do SNPs ... we need...

Thanks, but it seems to only do SNPs ... we need to annotate indels, too.
Forum: Bioinformatics 03-03-2011, 01:07 PM
Replies: 31
Views: 19,002
Posted By jnfass
We're looking at using Ensembl's Variant Effect...

We're looking at using Ensembl's Variant Effect Predictor right now ... but with a non-model organism (or at least a model organism with some regions replaced by a "better" assembly). It seems like...
Forum: Bioinformatics 02-08-2011, 11:59 AM
Replies: 6
Views: 2,455
Posted By jnfass
Thanks Laura! - Ensembl's Variation Effect...

Thanks Laura! - Ensembl's Variation Effect Predictor worked perfectly, and the online version is set up for Aribidopsis and about 8 other plants, so it didn't even require any hacking.

We talked...
Forum: Bioinformatics 02-04-2011, 12:22 PM
Replies: 6
Views: 2,455
Posted By jnfass
Thanks!

Thanks krobison, swbarnes,

I checked out your search results link, krobison ...
GAMES and MU2A seem to be limited to human (similarly for SNPnexus, which I just stumbled across), and MU2A is a...
Showing results 1 to 25 of 88

 


All times are GMT -8. The time now is 08:37 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO