User: thestaroceanster

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Posts by thestaroceanster

<prev • 12 results • page 1 of 2 • next >
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Comment: C: what does X means in bam2R result of deepSNV package?
... Thanks, that definitely solved that! ...
written 8 months ago by thestaroceanster0
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what does X means in bam2R result of deepSNV package?
...   Currently I am working with deepSNV and realized that the bam2R output results with A T C G X and N. I am aware of N stands for the reads that did not meet the threshold of quality, but I could not figure out what X stands for? I check the manual and the other information about it might be it sta ...
deepsnv written 9 months ago by thestaroceanster0 • updated 9 months ago by story.benjamin10
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Comment: C: Conflict in cnvr and cnvs result from cn.mops
... Thanks for the answer. However, I only use cn.mops for only one sample (1315_1). So there should not be a second individual. ...
written 2.3 years ago by thestaroceanster0
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Conflict in cnvr and cnvs result from cn.mops
... So currently I have been using cn.mops for CNV detection. The result for one sample is confusing since there is overlap between different CNV regions in cnvr output. It reads as follows:   seqnames start end width strand X1315_1.final.bam 1 1 144813741 ...
cn.mops written 2.4 years ago by thestaroceanster0 • updated 2.3 years ago by Günter Klambauer540
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Comment: C: cn.mops encounter negative width problem
... Thanks for the answer!  That was very helpful! ...
written 2.4 years ago by thestaroceanster0
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Comment: C: cn.mops encounter negative width problem
... I've checked my bed files, which showed that the starting position and end position are correct, with segments end always larger than segments start point. However, when I reviewed the whole bed files, I found that some segments are slightly disordered and sometimes overlapped (maybe because I used ...
written 2.4 years ago by thestaroceanster0
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cn.mops encounter negative width problem
... The problem occurred when I run referencecn.mops on paired exome sequencing data. Here is the command: resRef <- referencecn.mops(cases=X[,1],controls=X[,4],classes=c("CN0", "CN1", "CN2", "CN3", "CN4", "CN5", "CN6","CN7","CN8","CN16","CN32","CN64","CN128"),I = c(0.025, 0.5, 1, 1.5, 2, 2.5, 3, 3 ...
cn.mops referencecn.mops written 2.4 years ago by thestaroceanster0 • updated 2.4 years ago by Günter Klambauer540
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which cn.mops function should I use
... Currently, I am using cn.mops for detection of copy number variation in exome sequencing data. However, I encounter difficulty in choosing which function I should use. My project including tumor and corresponding control samples which point me to the referencecn.mops function while my sequencing dat ...
cn.mops written 2.4 years ago by thestaroceanster0 • updated 2.4 years ago by Günter Klambauer540
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Comment: C: CopywriteR can't finish calculating copy number
... Thanks for your answer. I also consider the possibility of too large bam files since this program ran fine with previous (and smaller) bam file. The problem seems to solve itself after I ran each sample per time but each run it required the system to be reboot (which I figure out after serveral fail ...
written 3.3 years ago by thestaroceanster0
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CopywriteR can't finish calculating copy number
... Hello. I'm trying to use copywriteR for calculating copy number across samples genome. My problem is that the program seem to be  running for  a short period of time until it suddenly stop and quit to cmd command line. After showing the message about my job would be ran on multiple cpu, there is n ...
bam copywriter written 3.3 years ago by thestaroceanster0 • updated 3.3 years ago by t.kuilman140

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