User: Peavil

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Peavil10
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Posts by Peavil

<prev • 13 results • page 1 of 2 • next >
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Why does mpileup tell me the starting and ending base of a read?
... Mpileup tells the start and end base with $ or ^. chr1 1374834 A 19 gggGgggGggggGgggGg^Sg ===95=>9>=?:8@@@859 chr1 1551927 T 32 .$..,,,,..,..,..,...,,,,...,,.... I34>>=>1>==9>69><<<=??;<<= I wonder what these things mean. * Why is it telling ...
samtools mpileup written 8 weeks ago by Peavil10
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Comment: C: What is mean that mpileup read depth (read count) 0?
... thank you. I think I was mistaken for a while! ...
written 8 weeks ago by Peavil10
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Answer: A: Oncotator v1.8.0.0 usage, download database.
... I could solve the problem. That's because I did not install Oncotator properly. After installing Oncotator properly, I was able to run the program with the new DB. ...
written 8 weeks ago by Peavil10
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What is mean that mpileup read depth (read count) 0?
... Hi, I finish preprocess a bam file like base recalibrator, mark duplicate, ... and then, I run samtools mpileup with the bam. Most are in the form below. chr1 1007432 g 30 .$,$.,,..AAa,.AAa,,AA.aAa.A..,a, 3>5>;::@]<>::==>>4E6>>=8876@6< But, I ...
samtools mpileup written 8 weeks ago by Peavil10 • updated 8 weeks ago by Devon Ryan63k
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Oncotator v1.8.0.0 usage, download database.
... Hi. I used oncotator v1.8.0.0 with old-version database, It was running well. But, when I downloaded new database(oncotator_v1_ds_April052016.tar.gz. ) at (http://gatkforums.broadinstitute.org/gatk/discussion/4154/howto-install-and-run-oncotator-for-the-first-time), It doesn't run, and then p ...
database oncotator broad tool written 10 weeks ago by Peavil10
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Comment: C: when bwa mem run with different thread, output.sam is different.
... i appreciate your help. thanks again !! ...
written 10 weeks ago by Peavil10
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Comment: C: when bwa mem run with different thread, output.sam is different.
... First, thanks for your information. I'm confused, if a different data are low quality, shouldn't it filtered on pipeline like 'base recalibrator'? when I run Mutect2 with two different mapping data from one sample, they resulted slightly different number of 'PASS' filtered mutation from Mutect2 o ...
written 10 weeks ago by Peavil10
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when bwa mem run with different thread, output.sam is different.
... Hi, I run bwa-mem with same sample, different number of thread. and then, output file(sam) is different. my bwa version is 0.7.13, I see the bwa notice (https://github.com/lh3/bwa/blob/master/NEWS.md) > Release 0.7.13 (23 Feburary 2016) > Fixed a potential bug in the multithreading mode ...
mem alignment bwa sequencing written 10 weeks ago by Peavil10 • updated 10 weeks ago by genomax224k
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Question about MEMo(Mutual exclusivity modules) program
... I run the MEMo sample, then I could get graph1(result of GBM) ![enter image description here][1] But In other paper using MEMo, I see the graph2 showing signal of Activation/Inactiviation. ![enter image description here][2] How do I get the second graph? Does it needs another program? or Does ...
software genome signaling pathway memo written 12 weeks ago by Peavil10
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Comment: C: Is it possible that 'samtools mpileup' embeded in JAVA program?
... mm... thanks, I try to do that. is it called by JNI? i try to call samtools on Java. ...
written 6 months ago by Peavil10

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