User: Sara
Sara • 40
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- New User
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Posts by Sara
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8
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104
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... 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? ...
3
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1
answer
149
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1
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... 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 ...
0
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0
answers
129
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... 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 ...
written 12 weeks ago by
Sara • 40
0
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1
answer
152
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1
answers
... @ ATpoint: thanks. do you know how I can find copy numbers (CNVs)? ...
written 12 weeks ago by
Sara • 40
0
votes
1
answer
152
views
1
answer
... 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 ...
1
vote
1
answer
119
views
1
answer
... 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? ...
written 3 months ago by
Sara • 40
• updated
3 months ago by
Pierre Lindenbaum ♦ 122k
0
votes
1
answer
543
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1
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... 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? ...
0
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2
answers
801
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2
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... 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
Sara • 40
0
votes
2
answers
801
views
2
answers
... 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? ...
1
vote
1
answer
612
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1
answer
... I have `Ribo-seq` data (also aligned them) and trying to isolate the in-frame reads. do you know how I can do that? ...
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
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