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Forum: Bioinformatics 08-08-2017, 12:34 PM
Replies: 5
Views: 2,003
Posted By gruberjd
best practices for organellar ID and purging?

Hi Brian-- Any tips on pipelines or documents that describe the best way to evaluate (and possibly purge) the organellar content of a batch of reads? (Googling didn't get me as far as I was expecting...
Forum: Genomic Resequencing 05-19-2017, 11:49 AM
Replies: 3
Views: 5,532
Posted By gruberjd
Brian-- Thanks. I'll give BBMap a shot and will...

Brian-- Thanks. I'll give BBMap a shot and will certainly report success if I find it!
Forum: Genomic Resequencing 05-18-2017, 03:15 PM
Replies: 3
Views: 5,532
Posted By gruberjd
Question Calling variants when mapping reads from different species than reference

Hi all,

My SNP calling pipeline seems to be poorly performing when tasked with mapping reads from a sample that is from a related species from the reference assembly. (This sort of thing is common...
Forum: Bioinformatics 10-18-2013, 11:23 PM
Replies: 2
Views: 1,414
Posted By gruberjd
joshua -- thanks for the answer. I think I'll...

joshua -- thanks for the answer. I think I'll have to sit down with a result to see what is being deleted, matched, etc to fully understand.

yes, i think you are right that you have to pipe the...
Forum: Bioinformatics 09-11-2013, 01:14 PM
Replies: 2
Views: 1,414
Posted By gruberjd
what is the gap column of GMAP output

Hello all--

Really simple, I hope simple to answer, question. What is the gap column in GMAP output? What do the codes mean? For example:

'M998 D1 M41 I1 M1506'

I've looked at the original...
Forum: Bioinformatics 04-16-2012, 11:17 AM
Replies: 4
Views: 1,811
Posted By gruberjd
thanks gaffa, the right search term is exactly...

thanks gaffa, the right search term is exactly what I needed and I didn't know 'mappability'... something definitely wasn't right about "uniqueness". Thanks!
Forum: Bioinformatics 04-16-2012, 11:15 AM
Replies: 5
Views: 3,312
Posted By gruberjd
I'm not sure what the exact specificities of the...

I'm not sure what the exact specificities of the new format are, but the 1:N:0 or 2:N:0 in the header denote what /1 and /2 used to. This wikipedia page is helpful:
...
Forum: Bioinformatics 04-16-2012, 09:09 AM
Replies: 4
Views: 1,811
Posted By gruberjd
Hi Twaddlac-- Thanks for the reply. I don't...

Hi Twaddlac--

Thanks for the reply. I don't think depth can get me all the way. Sometimes the depth is lower than "regular" sequence, but not always. It can also look normal or be higher (which...
Forum: Bioinformatics 04-16-2012, 08:34 AM
Replies: 4
Views: 1,811
Posted By gruberjd
annotation of local sequence "uniqueness"

Hi all-- I am attempting to filter out false "SNPs" in my bowtie assemblies (yeast genomic DNA). One major predictor of SNP falseness is being located in a regions that shows sequence similarity with...
Forum: Illumina/Solexa 03-28-2012, 10:44 AM
Replies: 6
Views: 6,811
Posted By gruberjd
Sai-- there are a number of post-casava tools...

Sai-- there are a number of post-casava tools (mostly free) that can do this. For example, the fastx toolkit's barcode splitter works:
...
Forum: Sample Prep / Library Generation 02-16-2012, 08:40 AM
Replies: 9
Views: 7,789
Posted By gruberjd
Hi all (especially Jon Keats)-- Thanks for all...

Hi all (especially Jon Keats)-- Thanks for all the participation in the thread. I also love the Qiagen Gentra Puregene kit for DNA extractions, but it seems that the dsDNA content (from Qubit) is...
Forum: Bioinformatics 01-31-2012, 11:23 AM
Replies: 7
Views: 2,843
Posted By gruberjd
Christoph and HESmith-- can I ask, what DNA...

Christoph and HESmith-- can I ask, what DNA extraction technique do you favor for yeast? I have gotten good results with a very baroque, old school protocol, but I need to do several hundred...
Forum: Introductions 12-06-2011, 10:27 AM
Replies: 373
Views: 140,283
Posted By gruberjd
Hi everyone-- I'm a postdoc at the University of...

Hi everyone-- I'm a postdoc at the University of Michigan, we're beginning to sequence the genomes of yeasts that have been mutagenized and as a result show changes in gene expression. Step 1,...
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