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Search: Posts Made By: DavyK
Forum: Bioinformatics 08-29-2013, 03:14 AM
Replies: 0
Views: 1,790
Posted By DavyK
Ion torrent PCR duplicates

Hi All,

I am looking at some targeted ion torrent sequencing data. Over 90% of mapped reads are PCR duplicates. Is this normal? I thought it might be because the target is very small (11kb, 16...
Forum: Bioinformatics 01-17-2013, 10:25 AM
Replies: 3
Views: 4,892
Posted By DavyK
Yes, filtering is clearly important, although you...

Yes, filtering is clearly important, although you should always filter before comparing a two sample groups. Then you get into the issue of adjusting your filters based on what you see in a case vs...
Forum: Bioinformatics 01-07-2013, 04:53 AM
Replies: 3
Views: 4,892
Posted By DavyK
Filtering multisample vcf files on DP

Hi All,
I have a multi-sample VCF file produced by the GATK Unified Genotyper. I need to now filter these variants for SNPs that have a DP < 10. However the DP entry in the info field for a...
Forum: Bioinformatics 12-12-2012, 02:39 PM
Replies: 33
Views: 12,781
Posted By DavyK
Yeah I might try using a 0.5.x version and...

Yeah I might try using a 0.5.x version and compare the alignments to see if the upgrade is worth it.
Forum: Bioinformatics 12-12-2012, 02:18 AM
Replies: 33
Views: 12,781
Posted By DavyK
I have only recently discovered this problem. ...

I have only recently discovered this problem.
Compiling using make runs ok, no errors.
Indexing (human_g1k_v37 from the GATK website) on mac takes around an hour, as standard (I think).
bwa aln...
Forum: Bioinformatics 12-10-2012, 05:56 AM
Replies: 2
Views: 2,490
Posted By DavyK
sam 2 bam conversion error

Hi all, Just aligned some exome sequencing data for an individual, and when converting from sam to bam I get this error:

samtools view -h -S -b -o 1001-1.bam 1001-1.sam
[samopen] SAM header is...
Forum: Bioinformatics 09-13-2012, 03:16 AM
Replies: 1
Views: 1,196
Posted By DavyK
Samtools view region ftp

Hi all,
I know that samtools view can pull down data from the web on public http and ftp sites, that are not protected. But can it handle data that are on password protected ftp sites?
Does anyone...
Forum: General 09-05-2012, 03:01 AM
Replies: 1
Views: 2,837
Posted By DavyK
Import error after installing Pysam

Hi all,
I now there are a couple of threads asking about installing pysam already, and I tried the solutions posted there to no avail.

I am trying in install pysam on my MAC running OSX 10.7 with...
Forum: Bioinformatics 06-22-2012, 05:13 AM
Replies: 1
Views: 1,448
Posted By DavyK
bwa index from reference with unusual chromosomes

A similar question to http://seqanswers.com/forums/showthread.php?t=8951

I'm about to create my reference index for aligning some exome data. I wonder should I includes these chromosomes in the...
Showing results 1 to 9 of 9

 


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