BAM file into R from Illumina
1
0
Entering edit mode
@soheilazareie-15508
Last seen 5.5 years ago
Canada, Vancouver, University of Britis…

I have 49 bam files aligned by STAR through Illumina and just wondering if there is any way to export BAM files from illumina without downloading, for example into R, if someone helps me to understand how to load my files into a single read table through summarizeOverlaps I would really appreciate.

Thanks,

bam file STAR Illumina • 1.0k views
ADD COMMENT
0
Entering edit mode

thanks, but how it will detect the URL (I mean the exact path), in this code?

ADD REPLY
0
Entering edit mode
ta_awwad ▴ 10
@ta_awwad-11382
Last seen 20 days ago
Frankfurt am Main
myBam <-c ("trt_1.bam", "trt_2.bam",  "wt_1.bam","wt_2.bam")

bamLst <- BamFileList (myBam, yieldSize=2000000)

summarizeOverlaps(bamLst,......)

 

good luck

 

 

 

 

 

 

 

 

ADD COMMENT

Login before adding your answer.

Traffic: 735 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6