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Search: Posts Made By: SamH
Forum: Academic/Non-Profit Jobs 10-29-2018, 10:59 AM
Replies: 0
Views: 305
Posted By SamH
Bioinformatics Data Scientist, University of Idaho

The Bioinformatics Scientist will contribute to and maintain high throughput data analysis systems to support the Genomics Resources Core (GRC) within the Institute of Bioinformatics and Evolutionary...
Forum: Academic/Non-Profit Jobs 10-06-2014, 12:09 PM
Replies: 0
Views: 604
Posted By SamH
Director, Comp. Resources Core, University of Idaho

Dear SEQanswers users, please see the following job posting:

https://uidaho.peopleadmin.com/postings/6114

We are seeking a motivated and enthusiastic person to fill the role of Computational...
Forum: Illumina/Solexa 01-08-2014, 08:25 PM
Replies: 10
Views: 4,251
Posted By SamH
I'm probably late to this party, but if you are...

I'm probably late to this party, but if you are still working on this problem, I've had very good luck doing the following:

1) screen duplicates, there are lots of tools, but I'm partial to...
Forum: Illumina/Solexa 07-06-2013, 02:51 AM
Replies: 6
Views: 1,878
Posted By SamH
Why no 454?

Why no 454?
Forum: Academic/Non-Profit Jobs 05-17-2013, 03:02 PM
Replies: 0
Views: 770
Posted By SamH
Washington State University: Computational Biology and Comparative Genomics

Please see the following link:
https://www.wsujobs.com/applicants/Central?quickFind=58322

This position seeks an experienced and motivated scientist with a comprehensive background in...
Forum: Bioinformatics 02-08-2013, 01:56 PM
Replies: 7
Views: 9,948
Posted By SamH
using bgzf for BAM files?

Hi All,
I wonder, has anyone tried using the Biopython bgzf support for parsing BAM files?
Specifically it would be nice to access a BAM line by line, however it doesn't seem to quite work...
Forum: Academic/Non-Profit Jobs 12-06-2012, 02:36 PM
Replies: 0
Views: 1,917
Posted By SamH
Systems Administrator for Bioinformatics Core

Please see job posting here: https://www.sites.uidaho.edu/AppTrack/Agency/Applicant/ViewAnnouncement.asp?announcement_no=13066052735

We look forward to seeing your application!

Sam
Forum: Academic/Non-Profit Jobs 08-27-2012, 08:39 AM
Replies: 0
Views: 824
Posted By SamH
Data Scientist (bioinformatics): University of Idaho

See job posting here: https://www.sites.uidaho.edu/AppTrack/Agency/Applicant/ViewAnnouncement.asp?announcement_no=12511023117

We look forward to seeing your application!

Sam
Forum: Bioinformatics 01-17-2012, 02:16 PM
Replies: 3
Views: 3,691
Posted By SamH
Yeah, adding -B made that SNP appear: ...

Yeah, adding -B made that SNP appear:

NC_015433.1_Ss_ST3 569984 . A C 999 . DP=1328;VDB=0.0735;AF1=1;AC1=6;DP4=0,0,657,577;MQ=37;FQ=-288 GT:PL:GQ ...
Forum: Bioinformatics 01-11-2012, 04:56 PM
Replies: 3
Views: 3,691
Posted By SamH
Post samtools/bcftools missing obvious SNPs?

Hi, I am having some trouble with what appears to be missed calls for SNPs while using the samtools/bcftools package.
I am using the latest release samtools 0.1.18 (r982:295), and bcftools...
Forum: Ion Torrent 09-09-2011, 05:10 PM
Replies: 15
Views: 6,201
Posted By SamH
What happened when you ran Ion Torrent FASTQ...

What happened when you ran Ion Torrent FASTQ files through Newbler 2.6? It seems like it is handling some fastq files I fed it okay... but am I in for a bad surprise when the assembly finishes?
...
Forum: Bioinformatics 05-13-2011, 05:16 PM
Replies: 24
Views: 28,566
Posted By SamH
Isolated B's

Hi, hopefully I can revive this old thread for a little. I just got a big dataset from a HiSeq2000 machine at Berkeley, I'm not sure which version of the Illumina pipeline was used, but I do see...
Forum: Bioinformatics 05-06-2011, 03:29 PM
Replies: 5
Views: 9,011
Posted By SamH
Thanks for the suggestions! After digging...

Thanks for the suggestions!

After digging around a little more , I've figure out that bwa truncates the fasta reference ID at the first space, samtools mpileup doesn't handle this well and...
Forum: Bioinformatics 05-05-2011, 11:01 AM
Replies: 5
Views: 9,011
Posted By SamH
Hi, thanks for the tip! I re-ran everything...

Hi, thanks for the tip! I re-ran everything after substituting a more simple name into the reference fasta file, and it worked as expected.

SamH
Forum: Bioinformatics 05-04-2011, 10:07 AM
Replies: 5
Views: 9,011
Posted By SamH
samtools pileup vs mpileup for computing per-base coverage

Hi all, I have searched seqanswers and can't find anything directly addressing this, so hopefully someone can help me out a little bit.

I am working at getting coverage information using mpileup...
Forum: 454 Pyrosequencing 03-22-2011, 09:51 AM
Replies: 30
Views: 21,125
Posted By SamH
This worked perfectly for me! Thanks!

This worked perfectly for me!

Thanks!
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