User: mhasa006

gravatar for mhasa006
mhasa00630
Reputation:
30
Status:
New User
Location:
United States
Last seen:
1 week, 2 days ago
Joined:
3 years, 9 months ago
Email:
m*******@ucr.edu

Posts by mhasa006

<prev • 25 results • page 1 of 3 • next >
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Cancer data download with normal sample
... I want to download cancer dataset that contains some normal (control) samples too. Right now I can download data from [BoradInstitute][1] but I believe the dataset only contains cancerous patients information. For example, I need to download Breast cancer methylation dataset where I can have methyla ...
normal tcga cancer data cancer written 4 weeks ago by mhasa00630 • updated 29 days ago by Kevin Blighe37k
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Comment: C: BLAST against cancer genome
... I don't have the genomes. I am looking for cancer genomes. ...
written 3 months ago by mhasa00630
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Comment: C: BLAST against cancer genome
... I need to find if the gene is translocated. ...
written 3 months ago by mhasa00630
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BLAST against cancer genome
... I need to BLAST a particular gene against many cancer genomes. Is there a tool/webtool where I can do that? If not, where can I find the latest downloads of cancer genomes? I can run BLAST locally then. But I would prefer if there is a webtool for this. Thanks. ...
gene genome blast cancer written 3 months ago by mhasa00630 • updated 12 weeks ago by Biostar ♦♦ 20
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Efficient processing of a read and its mate from bam file
... I have BAM file sorted based on the position. But to process each read, I also need to access its mate information. I'm using `htsjdk` package and right now, I'm accessing the mate information with `queryMate()`. However, `queryMate()` is extremely expensive and for large BAM file it is taking a lot ...
htsjdk java bam samtools sam written 6 months ago by mhasa00630 • updated 6 months ago by finswimmer9.8k
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Extract the mate pair information with htsjdk
... I have a BAM file sorted by position. I need to process a group of reads from the BAM file at a time. To process that, I need to access the mate pair of each of these read at the same time. Is there a way using `htsjdk` to access the mate pair information using the information of the other pair. I ...
htsjdk bam samtools written 6 months ago by mhasa00630 • updated 6 months ago by Pierre Lindenbaum116k
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Extract the SAM File header section
... How can I extract the header section of the SAM File with `htsjdk` package? Below is an example of a SAM File @HD VN:1.3 SO:coordinate @SQ SN:chr1 LN:248956422 @SQ SN:chr10 LN:133797422 @SQ SN:chr11 LN:135086622 XXX:111:312:1312 99 chr1 ...
htsjdk java bam samtools sam written 7 months ago by mhasa00630 • updated 7 months ago by Pierre Lindenbaum116k
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Forum: Cancer related problem with sequencing data and deep neural network
... I am fairly new to both Cancer research and Deep Neural Networks (DNN). I want to do some research mostly classification problem using the sequence data in the area of cancer research. Could anyone guide me towards the materials/publications I can read regarding this? I have tried to do cancer type ...
forum sequence rna-seq deep neural network cancer written 10 months ago by mhasa00630
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OG/Fusion, TSG/Fusion in CGC
... In Cancer Gene Census (CGC) dataset, ([cgc link][1], there is a column named Role in cancer. The values of this attributes are 'fusion', 'oncogene', 'oncogene, fusion', 'oncogene, TSG', 'TSG, fusion', 'oncogene, TSG'. What does the 'fusion' mean? Does this mean a mixture? Or a gene that sometimes ac ...
tsg cgc og cancer written 12 months ago by mhasa00630 • updated 12 months ago by Sean Davis25k
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Comment: C: Cancer research for computer science student
... Thanks for the good wishes. And it's he :-) ...
written 15 months ago by mhasa00630

Latest awards to mhasa006

Popular Question 5 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 9 months ago, created a question with more than 1,000 views. For Extract gff of a particular chromosome
Popular Question 12 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 15 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 2.6 years ago, created a question with more than 1,000 views. For PacBio data assembly with Celera

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