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Search: Posts Made By: OlgaMikh
Forum: Bioinformatics 04-25-2019, 07:40 AM
Replies: 0
Views: 1,685
Posted By OlgaMikh
Picard InsertSizeMetrics Output Interpretation

Hi,

I am looking at the data from my pilot Miseq Nano run performed on ATAC-seq libraries.
I wanted to see whether the fragment size distribution pattern corresponds to the one normally observed...
Forum: Illumina/Solexa 04-24-2019, 07:11 AM
Replies: 2
Views: 1,560
Posted By OlgaMikh
Thanks for your reply! What exactly are your...

Thanks for your reply! What exactly are your criteria to conclude that the sample "looks good"? Would you say that I don't need to worry if I don't see TSS enrichment in the bigwig file that I've...
Forum: Illumina/Solexa 04-24-2019, 04:01 AM
Replies: 2
Views: 1,560
Posted By OlgaMikh
QC of ATAC-seq libraries on MiSeq Nano

Hi all,

I have recently prepared a pool of 9 ATAC-seq libraries from mouse hearts and performed a MiSeq Nano run to validate my pooling calculations, as it's difficult to accurately quantify the...
Forum: Sample Prep / Library Generation 03-26-2019, 10:15 AM
Replies: 5
Views: 3,963
Posted By OlgaMikh
Hello, has any of you solved this issue? Would...

Hello, has any of you solved this issue? Would greatly appreciate your response. I am seeing the same with FACS sorted cardiomyocyte nuclei.
Forum: Illumina/Solexa 03-12-2019, 06:56 AM
Replies: 1
Views: 2,131
Posted By OlgaMikh
ATAC-seq library sequencing

Hi,

I am about to submit my first mouse ATAC-seq libraries for sequencing, but I have doubts regarding the number of libraries to pool in one 100bp paired-end HiSeq2500 Rapid Run.
The Buenostro...
Forum: Bioinformatics 02-12-2012, 01:22 AM
Replies: 2
Views: 1,515
Posted By OlgaMikh
Exclude variants in certain regions

Hi all,
I would be very greatful if somebody can advise me software which could exclude SNPs at known regions. My problem are the SNPs in primer sequences, I have to exclude them out my further...
Forum: Bioinformatics 02-07-2012, 05:06 AM
Replies: 4
Views: 5,789
Posted By OlgaMikh
Ok, thanks, Annovar really seems to be powerful. ...

Ok, thanks, Annovar really seems to be powerful.
As I understood i need to additionaly download hg19 snp132 file for annotation of hg19 data?
Forum: Bioinformatics 02-07-2012, 03:20 AM
Replies: 4
Views: 5,789
Posted By OlgaMikh
VarScan output to VCF

Hi all,
my question might seem simple but I'm new to NGS so please help me..!
I was working with VarScan programme, used "pileup2snp" option. The result is a txt file with a list of SNPs. Now I...
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