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

Analysing 20,000 histograms in R?

02 March 2016 3,338 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

How to add missing citation?

Dear colleagues, I have found that many authors have a concern regarding their missing citation in RG because often citation in RG is lower than google scholars. I also missed some citation...

26 February 2021 928 6 View

Centrality measures computation in Biblioshiny/ Vosviewer?

26 February 2021 7,279 2 View

How to obtain Contig sequence from BAM file?

I have use HISAT2 for alignment . Now i want to obtain contig sequence from from BAM file in galaxy server? I have used Samtools View. That is giving me some sequence but I am not sure whether it...

12 February 2021 3,262 4 View

Which and How to use teaching strategies and procedures to effectively integrate the four skills while teaching English Language Online?

As an inexperienced teacher in the field of online teaching, I have the fear of unconsciously ignoring one of the skills while focusing on not ignoring the other! Therefore, I wish to make use of...

09 February 2021 5,101 4 View

Consensus sequence from ClustalX?

I am doing multiple sequence alignment to design primer for my gene. Can anyone tell me how to select the consensus sequence after alignment. I am using ClustalX for the alignment.

04 February 2021 8,872 2 View

What are some properties of a proton in a static B-field?

I have some basic questions about the behavior of a charged particle in a static B-field. 1. Without a B-field, the particle has spin, with random orientation and spin frequency. a) What...

24 January 2021 1,389 3 View

Which is best tool for alignment of large bacterial sequence?

Hi! I need to align big fasta files (bacterial 16S) . I have tried to align them in some web-servers and freeware, but my files are too big to be run in there. I will be very glad if you could...

16 January 2021 1,266 4 View

How to solve it:qRT-PCR detects the expression of a gene in cells, but the CQ value is close to 35 ?

Sequence alignment results show there is no problem with the primer. Normal cq values for other genes indicated that the conditions for amplification were also correct.

29 December 2020 7,450 3 View

Add text at the beginning of a specific reference in Latex?

Hey researchers! The journal I'm submitting to wants datasets to be listed in the reference as [dataset] Authors; Year; Dataset title; Data repository ; Version; Persistent identifier (e.g....

18 November 2020 2,681 5 View

How to form a quasi-ominidirectional beam with antenna arrays?

For beam alignment (802.11.ad) in a mmWave MIMO system, the transmitter starts with a quasi-ominidirectional beam. My question is how to design the hybrid precoder for a quasi-ominidirectional...

11 November 2020 7,516 3 View