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Forum: Illumina/Solexa 03-14-2017, 12:04 AM
Replies: 2
Views: 1,570
Posted By KyuzoSeq
Question Manifest File for Whole Genome Sequencing

Hi,

I've been looking for the PCR regions or 'manifest file' for a whole genome sequencing kit? In an example there hundreds of WGS in 1000G project. They provide also exomes with BED files of...
Forum: Ion Torrent 11-19-2016, 01:30 PM
Replies: 3
Views: 4,922
Posted By KyuzoSeq
It's basically a variant analysis process. What I...

It's basically a variant analysis process. What I need is trimming sequences by primer sequences but we have no information a about primer sequences.
Forum: Ion Torrent 11-18-2016, 12:59 AM
Replies: 3
Views: 4,922
Posted By KyuzoSeq
Question Sequence Trimming without Knowing Primer Sequences

Hi,

I have an IonTorrent output but the provider doesn't want to give information about primer sequences. Instead it gives a bed file includes regions of interest. So if I do alignment and ...
Forum: Bioinformatics 10-14-2016, 12:04 PM
Replies: 6
Views: 3,146
Posted By KyuzoSeq
Question Do you know any source to help me about...

Do you know any source to help me about understanding this situation? I cannot imagine how chromosomal structure organized in digital sequence. Maternal and paternal chromosomes stay there ok but...
Forum: Bioinformatics 10-13-2016, 05:23 AM
Replies: 6
Views: 3,146
Posted By KyuzoSeq
So, how to decide which sets of chromosomes are...

So, how to decide which sets of chromosomes are taken?
Forum: Bioinformatics 10-13-2016, 02:17 AM
Replies: 6
Views: 3,146
Posted By KyuzoSeq
Question Does reference genome contains alleles?

Hi,

I'm really confused about this; we have two almost same copy of genes (alleles) so when sequencing the genome that means there must be two location for same gene right? Therefore, in an...
Forum: Bioinformatics 04-10-2015, 02:01 AM
Replies: 0
Views: 1,378
Posted By KyuzoSeq
Multi-reads of ChIP-Seq data

I cannot clearly understand why there are multireads in chip-seq data? What they mean?

If protein bind to specific sequence after experiment why we see both uniqe and multiple alignments?

It...
Forum: Bioinformatics 04-08-2015, 08:44 AM
Replies: 0
Views: 1,629
Posted By KyuzoSeq
Question Multi-Reads in ChIP-Seq Experiment

I would like to ask about known literature about multiple reads of ChIP-Seq analysis.

Commonly researchers use "uniqely" mapped reads in their work. They blink reads which are aligned multiple...
Forum: Bioinformatics 03-08-2015, 06:40 AM
Replies: 6
Views: 4,627
Posted By KyuzoSeq
Bowtie2 and MapQ Calculation

Hi

I'm going to ask about bowtie2's mapping quality calculation for ChIP-Seq data. For sequences which align multiple locations Bowtie2 gives the MAPQ 30. It says for multiple aligned sequences,...
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