User: CY

gravatar for CY
CY20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
1 day, 10 hours ago
Joined:
1 year, 9 months ago
Email:
c*******@gwmail.gwu.edu

Posts by CY

<prev • 29 results • page 1 of 3 • next >
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Detecting CNV can't cover aneuploidy situation
... CNV detection in cancer sample can be done based on either mapping distance of paired-end reads or read depth. However, The mapping distance strategy is not able to detect CNV in case of aneuploidy, right? Because aneuploidy produces CNV while the mapping distance of paired-end reads on each chromos ...
next-gen sequence cnv written 8 days ago by CY20 • updated 7 days ago by WouterDeCoster20k
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Best approach to quantify specific bacteria strain
... I have a project asking to quantify a specific bacteria strain from a sample using qPCR. First I need to design one or more primers. Since I am new to primer design, I got several questions while designing the protocol. 1. Should I use 16S hypervariable region as PCR template? 2. Should I use Prime ...
sequence alignment qpcr snp written 16 days ago by CY20
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RAM / cache usage in frequently use BI pipeline
... I think we all agree that RAM / cache consumption is a issue when launch a bioinformatics pipeline. I would like to open a discussion on which tools / steps demand high volume of RAM. I know STAR is pretty RAM consuming when load genomes (30gb). And indexing, sorting probably. Can anyone share som ...
alignment next-gen rna-seq snp written 23 days ago by CY20
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Comment: C: STAR genomeLoad issue
... Well, I retried it in your way and it worked. Thanks Ryan! ...
written 23 days ago by CY20
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Comment: C: What makes low frequency variants callers good at what they do?
... Thank you for the answer. I do variant calling a lot and often struggle with the choice of caller. Do you mind share some more details? What do you mean by "Another part is simply not hard-coding requirements and assumptions about ploidy and variant frequency distribution"? Also, I found most cal ...
written 23 days ago by CY20
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Distributed / parallel computing in bioinformatics
... I am new to clustering computing. I was trying to run my pipeline in EC2 cluster. However, that is not real distributed computing, right? The tasks are not being distributed. It is just running running the same or different separately on each node. So why distributed computing is rarely used in b ...
distributed computing bioinformatics written 24 days ago by CY20
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What makes low frequency variants callers good at what they do?
... Some tools (FreeBayes, LoFreq, VarScan...) claim that they are good at detecting low frequency variant. Can anyone share some insight on what makes them good at detecting low frequency variant? Really appreciate! ...
variant calling lofreq freebayes somatic mutation written 24 days ago by CY20
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Comment: C: STAR genomeLoad issue
... Actually I was running two samples almost simultaneously. I thought using LoadAndKeep or LoadAndExit (by the way, what is the difference between these two? I thought both of them are loading the index and keep it in cache) allows the first pipeline load the index and keep it in cache and the second ...
written 24 days ago by CY20
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Comment: C: STAR genomeLoad issue
... So LoadAndExit is the same as LoadAndKeep? Both of these keeps index in memory until run --genomeLoad Remove. Also, how does STAR know when all STAR jobs finish? I mean if I write a loop, how can STAR know which is the last one? ...
written 24 days ago by CY20
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STAR genomeLoad issue
... I ran STAR in a shared memory environment and tried --genomeLoad LoadAndKeep LoadAndRemove and LoadAndExit hoping one-time reference load can be used by all the samples. However, each sample still load its own reference and memory accumulates in cache and eventual killed job due to insufficient RAM. ...
rna-seq written 24 days ago by CY20 • updated 24 days ago by h.mon7.2k

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