User: fatima.m.zare
fatima.m.zare • 20
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Posts by fatima.m.zare
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... Can somebody tell me how can I implement HMM to detect CNV segments from read count signal using hmm R package? ...
written 9 months ago by
fatima.m.zare • 20
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... Thanks. Actually, I read your paper and your GitHub repository. I have bam file, reference fasta file. I want to realign the soft clipped bases of my bam file with BAW aligner. I think that I should use SoftClipsToSplitReads. Unfortunately, I don't know how should I do with your program. Could you ...
written 20 months ago by
fatima.m.zare • 20
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... I have a question regarding unmapped reads. From SRBreak paper: "If reads are aligned across breakpoints then some parts of them cannot be mapped the first time. These parts are denoted by the ‘S’ character in the CIGAR strings of these reads".
'S' shows Soft Clipping; the clipped nucleotides are ...
written 20 months ago by
fatima.m.zare • 20
• updated
20 months ago by
d-cameron • 2.1k
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... Actually I want write my own code. I want to know about the method that use loess output and do correction for read counts. but Thanks for your answer. I will look at them maybe I can find their methods. ...
written 2.9 years ago by
fatima.m.zare • 20
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... I read this post ( https://www.biostars.org/p/92744/#233742 ) and I am wondering how can I remove GC content bias with Loess regression?
...
written 2.9 years ago by
fatima.m.zare • 20
• updated
8 months ago by
Leon • 110
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... I am wondering how can I remove GC content bias with Loess regression?
...
written 2.9 years ago by
fatima.m.zare • 20
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... I am using human genome (hg19). can I generate by myself instead of using USCS? ...
written 2.9 years ago by
fatima.m.zare • 20
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... I want to remove mappability bias from my data (bam file) and so I should calculate mappability score first. Actually I want to have windows with size 100bp. Is there any way to calculate mappability score for each window? ...
written 2.9 years ago by
fatima.m.zare • 20
• updated
2.4 years ago by
mehran.karimzade • 170
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... in this command 50 is windows size? ...
written 2.9 years ago by
fatima.m.zare • 20
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Comment:
C: Regions of extreme GC content
... Do you know how can I compute mappability? I want to fix mappability bias and I need mappability like gc content. ...
written 2.9 years ago by
fatima.m.zare • 20
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For Correct GC bias using read counts and Loess regression method
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