23 Questions 8 Answers 0 Followers
Questions related from Ahsan Raza
I have big wig file of RNA seq and BS seq data.I want to calculate number of overlapping reads of RNA seq that covers the methylated CG. Which function should I use to count number of overlapps
04 April 2016 9,866 2 View
I am using pandas in Python. I have a dataframe: col1 col2 col3 col4 col5 col6 col7 Variance Mean chr1 1002 NA NA 2 3 4 ...
04 April 2016 6,776 1 View
I have RNA sequencing files and i want to check the gene expression of all genes from that file? I want to know how can i get genes from that rna sequence files? Although it is a basic question...
03 March 2016 5,769 5 View
I have 100 RN A seq samples and i have mapped them using tophat. but the alignmnet is so so. like given below: Left reads: Input : 24818 Mapped : 1562 ( 6.3% of input) of these: 122 ( 7.8%) have...
03 March 2016 7,800 4 View
I have RNA seq data which I have mapped using tophat. but the alignmnet of these sequences is very poor . How many aligned reads should be there for selection of RNA sequneces.can it be more than...
03 March 2016 9,658 5 View
I want to get the output of tophat in a new directory each time instead of its by default directory ./tophat_out. For this i have also added to tohat command -o directory_name but every time it...
03 March 2016 211 5 View
I want to gather methylation column from 100s of BS sequences files into a single file in a way that the first column should be the name of genes and the other 100 columns are the methylation...
03 March 2016 5,932 3 View
I am using Encode chipseq .bam file as a control and when i make tag directory of it by using homer s/w it gave me low enrichment with lots of background. Is this sample is good to use for...
03 March 2016 7,007 0 View
I am trying to intersect methylation data with promoter.bed. This promoter file I made from UCSC refseq gene and gene prediction.bed. 1 chr1 134212401 134213001 NM_001195025 0 +2 chr1 134212401...
03 March 2016 3,653 4 View
I have to map reads from RNA seq files to the methylated DNA sequence. How to find the reads that matches the methylated DNA seq? Does anyone have any idea?
03 March 2016 2,346 2 View
NM_001081462 chr5 134833230 134833830 0 - 12.5NM_001081463 chr5 134833230 134833830 0 - 12.5NM_001081464 chr5 134833230 134833830 0 - 12.5NM_001081465 chr5 134833230 134833830 0 - 12.5NM_001081466...
03 March 2016 2,176 1 View
I have 20,000 histograms and I want to analyse them for unimodal or bimodality. Do any one know about any R command to automatically analyse them in a single go?
03 March 2016 1,744 3 View
What does P value means and from what range to what is it significant? I have read a lot of web pages but haven't understood. Please immediate help is required. I need to interpret Hartigan...
03 March 2016 8,431 10 View
I have tophat out put and i have to find "The number of aligned reads whose mate pair was also aligned to the reference." from which file i can find this information as the align_summary.txt...
03 March 2016 6,954 0 View
rownames(Data)=as.character(Data[,1]) I am using this code:and Data[,1] has following output head(Data[,1])[1] "chrUn_random-1" "chrUn_random-2" "chrUn_random-3" "chrUn_random-7" [5]...
03 March 2016 3,650 3 View
I tried the following code to generate a hist and it apparently seems to be unimodal but still this dip.test shows non-uni modal. Please help me in this regard I am...
03 March 2016 3,326 1 View
Actually i have drawn 20,000 histograms . I have used dip test in R for checking bimodality and unimodality but I found results as follow:0.0139004602285866 1 76 non-unimodal, i.e., at least...
03 March 2016 9,961 0 View
I am quite new in this area and I dont understand what to do exactly.I have drawn 20,000 histograms by using for loop but i m not understanding how to analyse them together for unimodality and...
03 March 2016 3,408 1 View
Actually i have to check for effect of methylation on expression of each gene and i have rna seq and bs seq data can i do like: 1.download gene ids from UCSC browser and then intersectBed with...
03 March 2016 916 1 View
bismark [options] {-1 -2
02 February 2016 1,351 4 View
no index file is generated by default only CT and GA folders are generated. what to do?
02 February 2016 5,321 0 View
Does the data generated by ImageJ or Image studio Lite is publishable? How can we present our data produced by these softwares?
12 December 2015 3,751 2 View
I have to analyse the DNA bands on agarose gels by using Scion image software. How can I interpret the data of scion image software so that it can be published.can we apply stats on scion image...
12 December 2015 2,973 1 View
