User: Sara

gravatar for Sara
Sara40
Reputation:
40
Status:
New User
Location:
Last seen:
1 day ago
Joined:
3 years ago
Email:
a***********@yahoo.com

Posts by Sara

<prev • 32 results • page 1 of 4 • next >
8
votes
0
answers
104
views
0
answers
How safe the UCSC is for patients data
... I have some `DNAseq` data from patients and trying to load them the `UCSC`. but since the data is from patients and rules about the patients data is so strict I need to know if `UCSC` is really safe or not. do you know how safe the `UCSC` is for patients samples? ...
rna-seq written 3 days ago by Sara40 • updated 2 days ago by ATpoint21k
3
votes
1
answer
149
views
1
answer
getting error when indexing bam files
... I have aligned my fastq files to hg19 using this command: bwa mem hg19.fa /DATA/myfile.fastq.gz then I made bam files from sam files using: samtools view -Sb myfile.sam > myfile.bam then I sorted the bam files using: samtools sort myfile.bam myfile.sorted.bam and now I am tryin ...
genome alignment written 9 weeks ago by Sara40 • updated 9 weeks ago by swbarnes26.2k
0
votes
0
answers
129
views
0
answers
Comparing 2 methods to identify CNVs using WGS data
... I have 2 method to find CNVs using WGS (whole genome sequencing) data. for both of them I have calculated CNV z-score for every chromosome arm. now I want to compare these 2 methods to see which one is more precise to detect CNVs. so the question is: how can I compare these 2 methods considering the ...
genome written 12 weeks ago by Sara40
0
votes
1
answer
152
views
1
answers
Comment: C: visualizing the Shallow whole genome sequencing on the UCSC
... @ ATpoint: thanks. do you know how I can find copy numbers (CNVs)? ...
written 12 weeks ago by Sara40
0
votes
1
answer
152
views
1
answer
visualizing the Shallow whole genome sequencing on the UCSC
... I have a Shallow whole genome sequencing data set and aligned that using bwa. I am trying to visualize the data on the UCSC. first I made wig file but they are so big to be uploaded then I made bedgraph file and managed to upload them on the UCSC but the coverage is so low. here you find a screensho ...
genome written 12 weeks ago by Sara40 • updated 12 weeks ago by bernatgel2.0k
1
vote
1
answer
119
views
1
answer
read counts per chromosome arm
... I have `DNAseq` data and trying to get the read `counts per chromosome arm`. but I do not know the correct way. shall I align to every chromosome separately or the whole genome? how can I count the reads per chromosome arm? I mean what tool can I use for this goal? ...
genome alignment written 3 months ago by Sara40 • updated 3 months ago by Pierre Lindenbaum122k
0
votes
1
answer
543
views
1
answer
removing a part of sequence of all genes
... I have `3'-seq` data and planning to remove `polyA` of all genes. I have aligned the reads but I do not know how to remove `polyA` at the end of genes. do you know how to do that? ...
rna-seq written 22 months ago by Sara40 • updated 22 months ago by glihm600
0
votes
2
answers
801
views
2
answers
Comment: C: counting the reads that mapped to a part of transcriptome
... I can actually align to the part of transcriptome that I want (first I have to make fasta file and use it as reference file to align to). I can also make gtf file using the same file and count using that. but in both cases it returns 0 counts. so I thought maybe I should align to the genome and cou ...
written 22 months ago by Sara40
0
votes
2
answers
801
views
2
answers
counting the reads that mapped to a part of transcriptome
... I have `RNAseq` data and trying to count the reads that mapped only to a part of `5'UTR` (in fact the whole `5'UTR` except the first 50 `nts`). do you know how to do that? ...
rna-seq written 22 months ago by Sara40 • updated 22 months ago by glihm600
1
vote
1
answer
612
views
1
answer
isolating in frame reads from a file
... I have `Ribo-seq` data (also aligned them) and trying to isolate the in-frame reads. do you know how I can do that? ...
rna-seq written 22 months ago by Sara40 • updated 22 months ago by glihm600

Latest awards to Sara

Popular Question 8 months ago, created a question with more than 1,000 views. For identification of adapters from fastq file.
Popular Question 8 months ago, created a question with more than 1,000 views. For Isolating reads from specific region from bam file
Popular Question 8 months ago, created a question with more than 1,000 views. For how to visualize the RNAseq data on IGV
Popular Question 14 months ago, created a question with more than 1,000 views. For Isolating reads from specific region from bam file
Popular Question 14 months ago, created a question with more than 1,000 views. For filtering genes out from bam file using samtools
Popular Question 14 months ago, created a question with more than 1,000 views. For error in macs2 usage

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 648 users visited in the last hour