User: Nitha

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Nitha10
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New User
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5 months, 2 weeks ago
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4 years, 5 months ago
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Posts by Nitha

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Is there a FASTA file containing 1000 Genomes variant information to check refer
... @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 Nitha10
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Comment: C: Understanding Samtools Flagstat Output
... Thankyou@DevonRyan. Whether I have to delete this post and re-post as a new question? ...
written 8 months ago by Nitha10
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Answer: A: Understanding Samtools Flagstat Output
... @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 Nitha10
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samtools flagstat calculation
... 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 ...
samtools written 9 months ago by Nitha10 • updated 9 months ago by Devon Ryan95k
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Comment: C: how to calculate unique read coverage in WGS of human
... @h.mon Thank you very much for the detailed explanation. ...
written 12 months ago by Nitha10
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Comment: C: how to calculate unique read coverage in WGS of human
... @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 Nitha10
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Comment: C: how to calculate unique read coverage in WGS of human
... @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 Nitha10
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how to calculate unique read coverage in WGS of human
... 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 ...
sequencing wgs next-gen human illumina written 12 months ago by Nitha10 • updated 12 months ago by h.mon30k
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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 Nitha10
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Removing redundancy in structure level
... 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 ...
protein structure pdb modebase redundancy written 3.2 years ago by Nitha10

Latest awards to Nitha

Popular Question 7 months ago, created a question with more than 1,000 views. For strand bias, gram negative bacteria
Popular Question 7 months ago, created a question with more than 1,000 views. For strand bias, gram negative bacteria
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Correspondance Analysis by using CodonW- codon usage biase
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Genome & Protein Retrival
Popular Question 3.0 years ago, created a question with more than 1,000 views. For CLC workbench- subtractive genomics
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to plot ENc Vs GC3 graph
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Mauve tool, Genome alignment

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