User: Can Holyavkin

gravatar for Can Holyavkin
Can Holyavkin240
Reputation:
240
Status:
Trusted
Location:
Turkey
Last seen:
2 years, 10 months ago
Joined:
4 years, 1 month ago
Email:
c***********@icloud.com

Posts by Can Holyavkin

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Strange Pattern in Bam File
... **We solved the real cause of this pattern. It's duplication event of 200 bp area in that rectangular area.** We BLAST the unmapped parts of reads at the ends of rectangular area. And we found out that they are perfectly matched to region inside of this area. ![enter image description here][1] ...
written 2.8 years ago by Can Holyavkin240
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Comment: C: Strange Pattern in Bam File
... **Thank you John.** Now I will check all rest of these trimmed reads and see that if they are aligned to somewhere else. However, I couldn't understand that what kind of contamination may cause this pattern. ...
written 2.8 years ago by Can Holyavkin240
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Comment: C: Strange Pattern in Bam File
... **Dear Chris**, thank you for your reply. But we are not expecting cDNA in our sample. It's only PCR amplified (long-range primer set) products from genomic DNA. Also, I tried to remove repeats with built-in module of CLC Genomics Workbench. Unfortunately, it didn't change the coverage pattern at al ...
written 2.8 years ago by Can Holyavkin240
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Answer: A: Strange Pattern in Bam File
... **I repeated the alignment and realignment steps with BWA and GATK. The results are quite different now.** The upper image was taken after alignment+realignment of CLC genomics Workbench. The middle image was taken after alignment with BWA and realignment with GATK. The image in bottom was taken ...
written 2.8 years ago by Can Holyavkin240
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Comment: C: Strange Pattern in Bam File
... **Dear igor,** Actually you are right about uneven coverage of Nextera kits. We see such changes in especially in GC rich sites. However we did not come across such pattern in exome sequencing. As you know both of exome sequencing kits (Nextera Rapid Capture Exome) and Nextera kits use same transpos ...
written 2.8 years ago by Can Holyavkin240
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Strange Pattern in Bam File
... **We have encountered strange pattern in bam file that is generated from amplicon sequencing. (Nextera XT, illumina MiSeq).** As you can see at the middle of bam file, rectangular-shaped coverage is formed. Half of the reads finished at the right side of the rectangular; while other half of reads ...
alignment structural variant bam written 2.8 years ago by Can Holyavkin240
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Comment: C: How to bulk convert coding position of transkript to genomic positions?
... Wow. That was quick. :) Thank you Vivek. ...
written 3.7 years ago by Can Holyavkin240
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How to bulk convert coding position of transkript to genomic positions?
... I have several coding position (e.g c.124 or c.2432) of specific transcript. How can I convert these positions to genomic position for hg19 reference? ...
position written 3.7 years ago by Can Holyavkin240 • updated 3.7 years ago by Pierre Lindenbaum118k
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Comment: C: How to ignore bases with bcl2fastq2 --use-bases-mask
... :D Oh! Thank you.  ...
written 3.8 years ago by Can Holyavkin240
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How to ignore bases with bcl2fastq2 --use-bases-mask
... Hello, How can I ignore the first bases of index reads with bcl2fastq2 —use-bases-mask option?  The index read has 8 cycles, but I want to use only “last 7” of them. illumina bcl2fastq manual only mention about ignoring the last reads, not ignoring the first reads. I tried the following option bu ...
illumina bcl2fastq masking written 3.8 years ago by Can Holyavkin240 • updated 3.8 years ago by Dan D6.7k

Latest awards to Can Holyavkin

Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Strange Pattern in Bam File
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Strange Pattern in Bam File
Student 2.8 years ago, asked a question with at least 3 up-votes. For Population Frequency Data of Mitochondrial Variants
Scholar 2.8 years ago, created an answer that has been accepted. For A: Strange Pattern in Bam File
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: TruSeq Exome Enrichment Kit Targeted Regions BED File
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: TruSeq Exome Enrichment Kit Targeted Regions BED File
Student 3.8 years ago, asked a question with at least 3 up-votes. For Population Frequency Data of Mitochondrial Variants

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