Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: fatima.m.zare

gravatar for fatima.m.zare
Reputation:
20
Status:
New User
Location:
Last seen:
1 year ago
Joined:
3 years, 3 months ago
Email:
f************@gmail.com

Posts by fatima.m.zare

<prev • 18 results • page 1 of 2 • next >
0
votes
0
answers
354
views
0
answers
HMM for detecting CNVs from read count signal
... Can somebody tell me how can I implement HMM to detect CNV segments from read count signal using hmm R package? ...
readcount hmm cnv R written 13 months ago by fatima.m.zare • 20
0
votes
1
answer
1.3k
views
1
answers
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 23 months ago by fatima.m.zare • 20
5
votes
1
answer
1.3k
views
1
answer
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 24 months ago by fatima.m.zare • 20 • updated 24 months ago by d-cameron • 2.1k
0
votes
1
answer
1.9k
views
1
answers
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 3.2 years ago by fatima.m.zare • 20
3
votes
1
answer
1.9k
views
5 follow
1
answer
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 3.2 years ago by fatima.m.zare • 20 • updated 12 months ago by Leon • 110
0
votes
1
answer
7.1k
views
1
answers
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 3.2 years ago by fatima.m.zare • 20
0
votes
1
answer
1.3k
views
1
answers
Comment: C: calculate mappability score for each window
... I am using human genome (hg19). can I generate by myself instead of using USCS? ...
written 3.2 years ago by fatima.m.zare • 20
1
vote
1
answer
1.3k
views
5 follow
1
answer
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 3.2 years ago by fatima.m.zare • 20 • updated 2.7 years ago by mehran.karimzade • 180
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Mappability calculation after mapping with Bowtie2
... in this command 50 is windows size? ...
written 3.2 years ago by fatima.m.zare • 20
0
votes
1
answer
1.5k
views
1
answers
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 3.2 years ago by fatima.m.zare • 20

Latest awards to fatima.m.zare

Popular Question 18 months ago, created a question with more than 1,000 views. For Correct GC bias using read counts and Loess regression method
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1030 users visited in the last hour