How to count number of overlapping reads of RNA seq?

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

03 April 2016 9,795 2 View

Pandas in python?

03 April 2016 6,700 1 View

Low enrichment with lots of background in encode control?

02 March 2016 6,931 0 View

Promoter file duplicated entries?

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...

02 March 2016 2,098 1 View

RNA Sequncing sample selection?

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...

02 March 2016 7,723 4 View

RNA sequencing data?

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...

02 March 2016 9,579 5 View

Tophat output directory issue?

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...

02 March 2016 139 5 View

I have RNA sequencing files and i want to check the gene expression of all genes from that file. Can anyone help?

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...

02 March 2016 5,694 5 View

MAking a table in R?

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...

02 March 2016 5,862 3 View

Tophat output?

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...

02 March 2016 6,894 0 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

How to normalise data on OPM package from R Studio ?

Good afternoon, I recently used OmniLog from BIOLOG for my experimentations : I tested the metabolism of different strains on 2 types of plates. I have 16 strains of 3 different groups...

02 March 2021 3,584 1 View

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View