User: liuxiaomeng90

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Posts by liuxiaomeng90

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Can I calculate histonmodification density by xxx_treat_pileup.bdg - xxx_control_lambda.bdg?
... I run MACS2 by the following command: /data/Software/MACS2-2.0.10.20131216/build/scripts-2.7/macs2 callpeak -B -t $bam1 -c $bam2 -n $s --nomodel --extsize 180 --SPMR I want to remove input signal from the treatment. Can I just xxx_treat_pileup.bdg - xxx_control_lambda.bdg to get what I want? My s ...
macs2 written 5.5 years ago by liuxiaomeng9070 • updated 5.3 years ago by Biostar ♦♦ 20
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How MACS2 generate xxx_treat_pileup.bdg and xxx_control_lambda.bdg?
... I don't know what the third column of xxx_treat_pileup.bdg and xxx_control_lambda.bdg mean? Is it stand for the non-duplicate reads coverage of a single site? Thanks ...
macs2 written 5.5 years ago by liuxiaomeng9070
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Answer: A: what is different between TCGA samples and cases?
... I sent email to TCGA for help. And this is the specialist's answere: I have received your question regarding the difference between cases and samples in TCGA.  Each patient is considered a case.  Each patient can have more than one sample analyzed in TCGA data.  In the example you gave me, you will ...
written 5.5 years ago by liuxiaomeng9070
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what is different between TCGA samples and cases?
... I download GBM data from TCGA. It is showed that there are 508 cases in mRNA track. I download all of the TN data from UNC AgilentG4502A_07 track of level 3. I'm wondering why there are 532 filenames in FIL_SAMPLE_MAP.txt? Is it mean that 1 case was sequenced several times? ...
tcga written 5.6 years ago by liuxiaomeng9070
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What is cy3 labeled sample from TCGA GBM data
... I downloaded GBM microarray data from TCGA website. When I open the expression files, I found two columns, the first one is gene symbol, the second is "log2 lowess normalized (cy5/cy3) ". Then I open the sdrf.txt file to find the explanation to the second column. It is said that cy5 is GBM and cy3 i ...
tcga written 5.6 years ago by liuxiaomeng9070
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Comment: C: Can I use RNA-seq data as control and microarray data as treatment to get differ
... Thank you! May be I will give up finding differentially expressed genes between microarray data and RNA-seq data. Your script help me a lot to learn using ComBat. It may be useful next time. ...
written 5.7 years ago by liuxiaomeng9070
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Comment: C: Can I use RNA-seq data as control and microarray data as treatment to get differ
... Thanks for your reply! I'd appreciate it if you give me your scripts of ComBat. It will be of great help to study microarray data. ...
written 5.7 years ago by liuxiaomeng9070
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Comment: C: Can I use RNA-seq data as control and microarray data as treatment to get differ
... I don't know if I can scale the RNA-seq data and microarray data as GSE64985 described, "performing quantile normalization on the entire compendium using the limma R package (version 2.18.2) in order to reconcile broader differences between datatsets and ensure that all arrays were on the same scale ...
written 5.7 years ago by liuxiaomeng9070
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How to find the binding sites for a particular transcription factor among the human genome
... I want to find the binding sites for a particular transcription factor among the whole genome. Maybe the results could be something like bed files which indicate the potential TFBS. I read some question about finding TFBS. But most of the question is about finding potential transcription factor in a ...
tfbs written 5.7 years ago by liuxiaomeng9070 • updated 5.7 years ago by Felix Francis510
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Comment: C: Can I use RNA-seq data as control and microarray data as treatment to get differ
... I am familiar with RNA-seq data but not with the microarray data and I find the document of ComBat is not detailed. The GEO data I used were some samples in GSE64985 which was normalized to obtain an integrated gene expression atlas across diverse biological sample types and conditions. What is supp ...
written 5.7 years ago by liuxiaomeng9070

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