SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Using split/merge .bams for Cufflinks DerSeb Bioinformatics 2 03-15-2012 10:42 AM
Somatic calling comparing differnt platform BAMs Mamun Bioinformatics 2 02-07-2012 06:24 AM
TCGA dbgap: where's the bams? Richard Finney Bioinformatics 0 06-13-2011 08:18 AM
Short Read Archive format problems Ender985 Bioinformatics 7 07-28-2010 11:23 AM
Error -- SPP package, MSER -- could you please help abmmki Introductions 0 11-15-2009 03:17 AM

Reply
 
Thread Tools
Old 10-12-2011, 02:27 AM   #1
EdinG
Junior Member
 
Location: Edinburgh

Join Date: Sep 2011
Posts: 3
Default Problems with SPP read.bams.tags

Hi,

I'm trying to use SPP to analyze chip-seq data. worked fine on a single bam file. Now, I wanted to combine 2 bam files and apply SPP to the merged set.

This is what I did:

samtools sort sorted1.bam file1.bam
samtools sort sorted2.bam file2.bam

samtools merge merged.bam sorted1.bam sorted2.bam
samtools index merged.bam

next in R:
>library("spp")
>chip.data=read.bam.tags("merged.bam")
BGZF ERROR: unable to open file merged.bam
ERROR: failed to open BAM file 'merged.bam'

Any ideas, what went wrong?
loading the initial files (file1, file2) was possible, the sorted ones, however could also not be loaded.

I checked with ScanBamParam and that was possible, too:

param <- ScanBamParam(what = what)
bam <- scanBam("merged.bam", param=param)

Any comment and help more than wellcome

Thanks

Last edited by EdinG; 04-09-2013 at 07:14 AM.
EdinG is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:39 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO