Forum: Bioinformatics
10-21-2013, 09:43 PM
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Replies: 6
Views: 2,319
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Forum: Bioinformatics
04-05-2013, 12:27 AM
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Replies: 6
Views: 2,319
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Forum: Bioinformatics
04-03-2013, 04:56 AM
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Replies: 6
Views: 2,319
so i tried this with a couple of my samples vs...
so i tried this with a couple of my samples vs human.... i'm getting only 3% not mapping. So there is either very little or no contamination in my sample. So then what can explain the bimodal gc...
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Forum: Bioinformatics
04-03-2013, 02:08 AM
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Replies: 6
Views: 2,319
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Forum: Bioinformatics
04-02-2013, 09:23 PM
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Replies: 6
Views: 2,319
Contamination in my sample?
Hi all!
I just ran a 100bp PE human exome seq run in my lab and was looking at the fastqc results of my run. I am getting this weird pattern in the gc content distribution and was wondering is...
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Forum: Bioinformatics
03-19-2013, 06:25 AM
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Replies: 14
Views: 25,653
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Forum: Bioinformatics
10-17-2012, 12:12 AM
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Replies: 1
Views: 1,763
FASTQC help
I'm not a java programmer so I need some help doing something I hope there's someone here who can assist!
According to the fastqc documentation, for calculating duplication levels it considers...
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Forum: RNA Sequencing
10-17-2012, 12:00 AM
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Replies: 3
Views: 1,328
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Forum: Bioinformatics
10-15-2012, 10:10 PM
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Replies: 8
Views: 6,622
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Forum: Bioinformatics
10-15-2012, 07:34 AM
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Replies: 8
Views: 6,622
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Forum: Illumina/Solexa
10-15-2012, 05:44 AM
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Replies: 3
Views: 2,294
What he means is that if you haven't provided a...
What he means is that if you haven't provided a samplesheet.csv (and if tehre wasn't one in your sequencing directory) then CASAVA will not register multiplexed lanes and all samples in a multiplexed...
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Forum: Bioinformatics
10-15-2012, 05:34 AM
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Replies: 4
Views: 1,299
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Forum: Bioinformatics
10-15-2012, 04:29 AM
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Replies: 8
Views: 5,709
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Forum: Sample Prep / Library Generation
09-27-2012, 06:11 AM
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Replies: 3
Views: 4,767
Bioanalyzer expired RNA Nano 6000 kit
Hey!
I'm need to run a preliminary QC on my RNA samples but I've got a problem... My RNA Nano 6000 kit expired in june 2010 (yes yes lmao :D ).
I wanted to know whether only reagents have an...
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Forum: Bioinformatics
08-08-2012, 11:55 PM
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Replies: 1
Views: 1,292
dbsnp rod file for hg19
Hey!
So i want to run GATK tools on y data which i've aligned to hg19 and i need the dbsnp rod file for hg19 (i believe it's dbsnp_132_hg19.rod right?) but i can't find it anywhere :mad:
the...
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Forum: Bioinformatics
07-31-2012, 12:30 AM
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Replies: 4
Views: 1,505
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Forum: Bioinformatics
07-30-2012, 09:04 PM
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Replies: 5
Views: 5,283
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Forum: Bioinformatics
07-30-2012, 08:58 PM
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Replies: 4
Views: 1,505
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Forum: Bioinformatics
07-30-2012, 04:34 AM
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Replies: 5
Views: 5,283
It seems to be the same sample in different...
It seems to be the same sample in different lanes/runs... so you can either merge the fastqs and align or align the 3 separately and merge the sams! I recommend the latter as it will take less time...
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Forum: Bioinformatics
07-30-2012, 02:49 AM
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Replies: 5
Views: 5,283
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Forum: Bioinformatics
07-30-2012, 02:38 AM
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Replies: 4
Views: 1,505
Perplexed!
Ok so this isn't really a problem per-say but i was just curious as to what it really means....
I ran picsrd's insert size metrics on my PE RNA Seq data (mapped to the Ensembl Transcriptome model)...
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Forum: Bioinformatics
07-18-2012, 12:30 AM
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Replies: 1
Views: 848
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Forum: Bioinformatics
07-03-2012, 09:26 PM
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Replies: 3
Views: 1,365
You can extract reads from a given region from...
You can extract reads from a given region from your sam/bam file. about assembling it ... u should be assemble it into a gene but about getting two haplotypes i can't say because then you would need...
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Forum: Bioinformatics
07-03-2012, 09:18 PM
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Replies: 7
Views: 5,169
Sorry there my mistake... when you said you...
Sorry there my mistake... when you said you aligned genomes i automatically thought in terms of fastq onto ref fast alignment stored in the form of bams.
So in my opinion, what you CAN do instead...
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Forum: Bioinformatics
07-02-2012, 08:59 PM
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Replies: 4
Views: 1,268
Hmmm... you can try what they did in that...
Hmmm... you can try what they did in that paper.... align with strict criteria i guess to get better results... i'm not sure about RNA seq aligning but as i said, when i aligned DNA reads from a non...
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