User: Nitha
Nitha • 10
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Posts by Nitha
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... @rodd I am also facing same issue, as per @ chrchang523 reply I had tried using reference from "http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use" but still the problem persist.
I have some doubts in understanding the checkVCF.py report, could anyone please anyone please help me ...
written 5 months ago by
Nitha • 10
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... Thankyou@DevonRyan. Whether I have to delete this post and re-post as a new question? ...
written 8 months ago by
Nitha • 10
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... @Devon Ryan, I had used two bam files of same samples (bam file obtained by two different ways 1. By using joined fastq files as input and 2. By using each fastq files for each steps) for alignment quality check using samtools falg stat. But i observed difference in duplicate numbers.
The .bam fi ...
written 8 months ago by
Nitha • 10
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... Hi all,
I have a doubt in samtools flagstat calculation, alignment quality check was done for the same samples but the alignment was done in different ways. Downloaded public available sample it was 80Gb fastq with Lane 1 and lane 2 which forward and reverse reads (paired end).
1. merged reads la ...
written 9 months ago by
Nitha • 10
• updated
9 months ago by
Devon Ryan ♦ 95k
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... @h.mon Thank you very much for the detailed explanation. ...
written 12 months ago by
Nitha • 10
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... @h.mon Thanks you. I am using paired end sequence. Now the above link is working, could you please explain how the illumina calculating the coverage, and what they mentioning about the unique reads.
How Does Illumina Calculate Human
WGS Coverage?
Illumina defines sequencing coverage as “the average
...
written 12 months ago by
Nitha • 10
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... @genomax The link which had given is the technical note, which I had mentioned in my post. I couldn't understand the statement in the technical note [Illumina defines sequencing coverage as “the average coverage of unique reads across the non-N portion of the human genome.”]. could you explain it. ...
written 12 months ago by
Nitha • 10
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... Hi All,
I have to calculate the coverage for human WGS of illumina sequenced read. After reading the technique note of illumina I have some doubts in WGS coverage calculation of human sequence.
( https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-30x-cove ...
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Comment:
C: Human Protein Structure Download
... Thank you. yes I have downloaded the available structures and remaining structures downloaded from ModBase. ...
written 3.2 years ago by
Nitha • 10
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... Hi All,
I have downloaded all available human proteome structure from PDB, normally there will be redundancy in structures (Different structures are deposited in PDB for single protein, how to download only non-redundant best models in bulk), facing trouble in removing the redundancy in structure l ...
written 3.2 years ago by
Nitha • 10
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