User: prakash

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prakash0
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Posts by prakash

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Cuffnorm: which output file should I use
... genes.fpkm_tracking is the file for genes with its normalized FPKM (fragment per kb per millions of mapped reads) ...
written 15 hours ago by prakash0
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Comment: C: Samtools rmdup and Piccard Markduplicates
... I have edited my query. ...
written 5 days ago by prakash0
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Samtools rmdup and Piccard Markduplicates
... Hello Bio Stars, I have doubt regarding duplicate removal from BAM file. I used two tools "**samtools rmdup**" and **Piccard MarkDuplicates**. I would like to understand why both of the tools remove different amount of duplicate reads. The document says: The **MarkDuplicates** tool works by com ...
alignment next-gen written 6 days ago by prakash0 • updated 5 days ago by Vijay Lakhujani1.1k
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Comment: C: PCR duplicates in RNASeq
... Thank you geek_y ! So if rmdup is removing duplicates, it indicate that my sample has duplicates. I understand duplicate removal is not an good idea for differential expression study, but is it not necessary to remove for Alternate splicing analysis. ...
written 10 days ago by prakash0
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PCR duplicates in RNASeq
... Hello Bio stars, I have small query regarding identification and removal of PCR duplicates from RNASeq data. The Tophat2 alignment stats calculated from samtool flagstat shows that there is no PCR duplicates (below alignment stats), but when I used samtools rmdup , it removes significant amount of ...
forum rna-seq written 10 days ago by prakash0 • updated 10 days ago by geek_y7.8k
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Different FPKM values for same condition form cufflink
... Hi all, I want to understand why cufflink give different FPKM value for same condition (say A) when comparing with two different condition (say B and C) after analysing separately (A vs B and A vs C). Is it possible to calculate FPKM separately for each condition and then calcualate the fold change ...
rna-seq written 11 months ago by prakash0 • updated 11 months ago by genomax32k
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Finding instances of motifs near peaks
... Hi I want to find instances of peaks near motif. I am using annotatePeaks.pl of HOMER. there is one option "-m <motif file1> <motif file 2>...". Can anybody tell me what would be the format of this file. Thanks in advance.   ...
chip-seq written 21 months ago by prakash0 • updated 21 months ago by Alex Reynolds20k
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Answer: A: Cuffdiff for differential gene expression
... I think you should go like this : For each condition you generate "transcript .gtf" 1. cufflinks -o output_file -G reference_GTF_file bam_file Then merge all the transcript.gtf of condition for which you want differential gene expression. cuffmerge -o output_file -g reference_GTF_file transcript ...
written 22 months ago by prakash0
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Comment: C: how to get p value for a set of fdr value
... Thanks Carl and Manuel for discussion !! I am going to try the method which Carl has mentioned. as i already have correlation coefficient value and several numbers of permutations because 1000 or 10000 permutations would be really computationally expensive. I have taken 6 permutations. that would ...
written 22 months ago by prakash0
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Comment: C: how to get p value for a set of fdr value
... Actually I am comparing two CHIPseq peak file. So here I am just comparing coordinates by checking overlap. Suppose if all coordinates of A overlaps with B that we can say correlation is 1. So like that comparison has been done. In order to assess that correlation is significant or not I have random ...
written 22 months ago by prakash0

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Popular Question 4 days ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value

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