User: akhattri

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akhattri0
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Posts by akhattri

<prev • 12 results • page 1 of 2 • next >
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How to censor TCGA survial data for a specific number of days?
... We are analyzing some TCGA Overall Survival (OS) and Progression Free Interval (PFI) data. As for some cancer types the OS could be very long as compared to others. Moreover, with a longer duration, the probability of events (death) due to unrelated reasons (like, due to a car accident) increases, a ...
survival tcga km plot censor written 7 months ago by akhattri0 • updated 5 months ago by Biostar ♦♦ 20
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Can I convert two fields (4 digits resolution) HLA typing results to G group?
... I have done HLA typing using exome sequencing data. I have two questions in this regad: (i) Can I discard the extra fields and consider just first four digits (2 fields) or do I need to do any conversion. Example **A*01:01:01:01, A*01:01:01:02N, A*01:01:01:04, A*01:01:01:03** etc will become **A*0 ...
exome ngs hla typing hla written 4.0 years ago by akhattri0
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Does whole exome bam files in TCGA have unpaired reads?
... I am trying to slice some whole exome bam files from TCGA and for my pipeline I need to extract read pairs. I used samtools sort -n to sort the bam file and using bedtools bamtofastq to extract paired reads but it seems there are lot of reads for which there is no mate in the bam file. I thought I ...
exome ngs tcga bam written 4.0 years ago by akhattri0
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Comment: C: Extracting Read Pairs From Region So That All Pairs Remain Intact
... Could you figure out the solution to this problem? I am trying to do something similar: I want to extract the reads mapping to my region of interest and also extract it's pair even if is mapped out of region or unmapped. What I am trying to do is: (i) extracting the read names which map to the regi ...
written 4.0 years ago by akhattri0
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Comment: C: Viral load estimation from WXS (whole exome sequencing) data
... Yes that was my concern also. The thing is data is publicly available (TCGA) so I can not do anything. I was thinking if there is anyway to still do it with exome data. ...
written 4.1 years ago by akhattri0
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Comment: C: Viral load estimation from WXS (whole exome sequencing) data
... Seems it would only detect presence of HPV. I wanted to estimate the viral load. ...
written 4.1 years ago by akhattri0
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Answer: A: How to select columns from the dataframe based on variables from another datafra
... Thanks!! I am looking into SummarizedExperiment. Using dplyr: >df1 %>% select(one_of(dput(as.character(df2$Header)))) or >list.df2 <- dput(as.character(df2$Header)) >df1 %>% select(one_of(list.df2)) worked ...
written 4.2 years ago by akhattri0
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How to select columns from the dataframe based on variables from another dataframe
... I have a dataframe in which each column is microarray data of a sample. I want to select columns based on another dataframe (df2). I was trying to do it using select function of dplyr but somehow it does not work. df1 >head(df1) probeID WT.GS1 WT.GS2 WT.GS3 KO.GS1 KO. ...
R dplyr written 4.2 years ago by akhattri0
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Comment: C: Viral load estimation from WXS (whole exome sequencing) data
... Yes I did post it there first but as no one replied I ended up posting here. I am trying to delete that post but unable to find option. ...
written 4.2 years ago by akhattri0
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Answer: A: Viral load estimation from WXS (whole exome sequencing) data
... Yes that was my concern also. The thing is data is publicly available (TCGA) so I can not do anything. I was thinking if there is anyway to still do it with exome data. ...
written 4.2 years ago by akhattri0

Latest awards to akhattri

Great Question 2.5 years ago, created a question with more than 5,000 views. For How to select columns from the dataframe based on variables from another dataframe
Epic Question 2.5 years ago, created a question with more than 10,000 views. For How to select columns from the dataframe based on variables from another dataframe
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Error In Using Viralfusionseq With The Test Data On Centos 5 System
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Viral load estimation from WXS (whole exome sequencing) data
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Can I convert two fields (4 digits resolution) HLA typing results to G group?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Error In Using Viralfusionseq With The Test Data On Centos 5 System
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Error In Using Viralfusionseq With The Test Data On Centos 5 System

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