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User: fatima.m.zare

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Posts by fatima.m.zare

<prev • 17 results • page 1 of 2 • next >
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Comment: C: How can I split the soft clipped reads and map the splitted reads again.
... 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 7 months ago by fatima.m.zare • 20
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How can I split the soft clipped reads and map the splitted reads again.
... 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 ...
unmapped reads soft clipped reads. split reads written 8 months ago by fatima.m.zare • 20 • updated 8 months ago by d-cameron • 1.9k
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Comment: C: Correct GC bias using read counts and Loess regression method
... 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 22 months ago by fatima.m.zare • 20
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Correct GC bias using read counts and Loess regression method
... 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? ...
gc bias gc content read counts loess written 22 months ago by fatima.m.zare • 20
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Comment: C: Compute Binned Gc-Normalized Read Counts From Bam File
... I am wondering how can I remove GC content bias with Loess regression? ...
written 22 months ago by fatima.m.zare • 20
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Comment: C: calculate mappability score for each window
... I am using human genome (hg19). can I generate by myself instead of using USCS? ...
written 22 months ago by fatima.m.zare • 20
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calculate mappability score for each window
... 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? ...
score bias mappability mappability bias written 22 months ago by fatima.m.zare • 20 • updated 16 months ago by mehran.karimzade • 140
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Comment: C: Mappability calculation after mapping with Bowtie2
... in this command 50 is windows size? ...
written 22 months 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 22 months ago by fatima.m.zare • 20
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Comment: C: Regions of extreme GC content
... I changed "chr1" to "1" and .... . then my error was fixed. ...
written 22 months ago by fatima.m.zare • 20

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