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Forum: Sample Prep / Library Generation 04-10-2013, 09:18 AM
Replies: 3
Views: 2,294
Posted By chongm
Hi I'm using the V5+ UTR protocol and I'm finding...

Hi I'm using the V5+ UTR protocol and I'm finding on average 54% reads on target +-100 bp, whereas in their datasheet, they show ~80% on target. Just based on my experience with enrichment kits in...
Forum: Bioinformatics 03-12-2013, 07:57 PM
Replies: 5
Views: 2,385
Posted By chongm
I see, whereas in the case of a deletion all...

I see, whereas in the case of a deletion all bases will map to the read reference.
Forum: Bioinformatics 03-12-2013, 07:47 PM
Replies: 5
Views: 2,385
Posted By chongm
Thanks for the reply. So biologically there is no...

Thanks for the reply. So biologically there is no reason for there to be more deletions than insertions and so this ratio should approach 1. This is probably a naiive question but why are insertions...
Forum: Bioinformatics 03-12-2013, 06:43 PM
Replies: 5
Views: 2,385
Posted By chongm
Expected insertion: deletion ratio for exome data?

Hi Everyone,

I am wondering what the expected insertion: deletion ratio is for your exomes? Right now I'm getting ~0.9 meaning deletions are a bit more common than insertions in the exome? Is...
Forum: Bioinformatics 03-12-2013, 12:40 PM
Replies: 1
Views: 2,785
Posted By chongm
Hi: If you're using GATK, you can check...

Hi:

If you're using GATK, you can check their bestpractices. They use "hard filters" like the ones you would be using for smaller experiments (in terms of either low depth or small # samples)
...
Forum: Bioinformatics 03-12-2013, 12:25 PM
Replies: 0
Views: 1,183
Posted By chongm
Strand Discordant Loci - GATK local Indel realignment

Hi Everyone:

I had a conceptual question regarding "strand discordant loci." In the local realignment video tutorial posted by GATK...
Forum: Illumina/Solexa 03-05-2013, 11:45 PM
Replies: 2
Views: 3,031
Posted By chongm
Truseq 62 Mb exome enrichment

With the 62 Mb exome enrichment, on a hiseq lane we 6-plexed and got ~70%PCTbases > 20x
Forum: Bioinformatics 03-05-2013, 11:25 PM
Replies: 0
Views: 1,393
Posted By chongm
Post Illumina Truseq Exome 62Mb - variant metrics?

Hey Everyone,

I'm just curious what kind of variant metrics everyone obtains for the Truseq 62 Mb exome enrichment. I've only processed around 6 samples but there are ~40 K SNPs per sample and...
Forum: Bioinformatics 03-05-2013, 10:04 AM
Replies: 6
Views: 2,452
Posted By chongm
Thanks for this insight Bukowski. I'll consider...

Thanks for this insight Bukowski. I'll consider the homopolymer signal benign then. But yes the hump is very strange.
Forum: Genomic Resequencing 03-05-2013, 07:59 AM
Replies: 2
Views: 3,583
Posted By chongm
I would suggest using a program known as FASTQC,...

I would suggest using a program known as FASTQC, which gives you a lot of summary metrics for read quality, GC content, duplication levels, overrepresented sequences. It's fast and provides very nice...
Forum: Bioinformatics 03-05-2013, 06:57 AM
Replies: 2
Views: 2,479
Posted By chongm
Okay this is much more clear to me now! Thanks a...

Okay this is much more clear to me now! Thanks a lot!
Forum: Bioinformatics 03-04-2013, 11:03 PM
Replies: 6
Views: 2,452
Posted By chongm
Hi Kcchan, Thanks for the explanation, but...

Hi Kcchan,

Thanks for the explanation, but I don't see any of my adapter sequences found in the overrepresented sequences section of FASTQC results. I only see "AAAAA" and "TTTTT" in this section...
Forum: Bioinformatics 03-04-2013, 07:24 PM
Replies: 6
Views: 2,452
Posted By chongm
The average insert size was ~360 bp. Why do reads...

The average insert size was ~360 bp. Why do reads go polyA or polyT when they've read through the entire length of the sequence?
Forum: Bioinformatics 03-04-2013, 06:40 PM
Replies: 6
Views: 2,452
Posted By chongm
Strange FASTQC Results - PerSequence GC Content

Hi Everyone:

I would be grateful if someone could take a quick look at these FASTQC results. This is exome-seq 100 bp paired-end data. For the most part, FASTQC results seem normal, except a...
Forum: Bioinformatics 03-04-2013, 05:40 PM
Replies: 2
Views: 2,479
Posted By chongm
DNA-seq and Read Trimming: Basic Question

Hi Everyone:

I am doing exome sequencing and I just had a basic question about read trimming. Is read trimming at the 3' end AND/OR by base quality score completely necessary? What influence will...
Forum: Bioinformatics 02-11-2013, 11:01 AM
Replies: 0
Views: 1,951
Posted By chongm
Picard Collect Insert Size Java Problem

Hi Everyone:

I was trying to generate histograms for insert size using Picard's "CollectInsertSizeMetrics" but came across an error.


I ran the following code:

java -Xmx4g...
Forum: Bioinformatics 02-08-2013, 02:22 PM
Replies: 9
Views: 19,821
Posted By chongm
Maybe your library has low complexity?

Maybe your library has low complexity?
Forum: Bioinformatics 01-18-2013, 07:37 AM
Replies: 0
Views: 843
Posted By chongm
Picard - Where have my reads gone?

Hi Everyone:

I had a question regarding the measure, PCT_PF_UQ_READS_ALIGNED, derived by calculatehsmetrics. I know that it is defined as "PF Reads Aligned / PF Reads". For one sample, this turns...
Forum: Bioinformatics 01-17-2013, 02:13 PM
Replies: 27
Views: 12,354
Posted By chongm
% reads on target does not equal % bp on target

I just wanted to note that Picard's hsmetrics will calculate the percentage of basepairs that map to target regions which isn't the same as the percentage of reads that map to target regions. e.g. if...
Forum: Bioinformatics 01-16-2013, 01:17 PM
Replies: 27
Views: 12,354
Posted By chongm
Thanks!

Thank you Jon_Keats! The -H seemed to have done the trick! :)

chongm
Forum: Bioinformatics 01-16-2013, 09:05 AM
Replies: 27
Views: 12,354
Posted By chongm
Has anyone used hsmetrics for Illumina truseq...

Has anyone used hsmetrics for Illumina truseq exome targets? I'm having issues running this (even though I'm using the same modified bed file - with header from samtools - for both target and bait...
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