Question: How to read .bam file in Rsamtools R package?
1
gravatar for M K
5.9 years ago by
M K490
United States
M K490 wrote:

I have an accepted_hits.bam file which is from tophat  ouput, and I need to use Rsamtools "R package" to do some analysis for the .bam file. So any one know how to read this file in R.

R • 14k views
ADD COMMENTlink written 5.9 years ago by M K490
2
gravatar for Danielk
5.9 years ago by
Danielk590
Karolinska Institutet, Stockholm, Sweden
Danielk590 wrote:

Did you try the package vignette?

http://www.bioconductor.org/packages/2.13/bioc/vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf

ADD COMMENTlink modified 9 weeks ago by RamRS25k • written 5.9 years ago by Danielk590

Hi Danielk, I used the Rsamtools package and I follow the the example in the pdf and it works. But I need to use my .bam file not the one provided in the pdf file. Also, I need to read all information in this file (not a portion).

ADD REPLYlink modified 9 weeks ago by RamRS25k • written 5.9 years ago by M K490
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1095 users visited in the last hour