Problem importing BAM files in Artemis

pasta · 02-08-2011, 07:47 AM

Hi there,

My first post here and that will be a question.

We got data from the Illumina platform and I used BWA to align my reads on the reference genome, which generated BAM files at the end. I would like to visualize my data using Artemis but I cannot load my BAM file. Indeed, I receive this message :
"failed to open Organism.pe.bam.SORTED.bam: cannot recognise format of binary file"

I dont understand why

... The BAM file seems to be OK since I managed to open it with a bunch of different software.
I do have the latest version of Artemis+ACT+ Java, and I did index and sort my BAM file.

Any help would be appreciated.

Thanks

Toni

pasta · 02-08-2011, 08:47 AM

Forget abt my question - I just figured it out myself

(whaoo, it took me exactly 1 hour LOL)

maubp · 02-08-2011, 10:17 AM

And what was the solution? Anyone else with the same problem will probably find this thread via Google.

Tani · 02-09-2011, 12:54 AM

Ensure that the corresponding .bai file in the same directory as of .bam file

pasta · 02-09-2011, 04:58 AM

I just did something stupid with Artemis... I tried to load the BAM file straight away without any genome loaded first .... I thought it was worth mentioning I was stupid LOL

Trudy · 04-04-2011, 06:32 AM

How do you solve this problem?
I have the same problem..Could you help me?

ARTEMIS doesn't load my bam file..
I sorted and indexed the file.bam with samtools.....but the problem persist!

help me please....

pasta · 04-04-2011, 08:45 AM

Quote:

Originally Posted by Trudy

How do you solve this problem?
I have the same problem..Could you help me?

ARTEMIS doesn't load my bam file..
I sorted and indexed the file.bam with samtools.....but the problem persist!

help me please....

Well, first load your Genbank file(s) on the startup window:
File > Open > select your files
Then, when your chromosome is loaded, on the new window simply choose:
File > Read BAM/VCF > select your file

Hope it helps !

Toni

coldturkey · 01-31-2012, 06:26 AM

I don't have a problem opening bam and vcf files in artemis, however, I would like to open multiple vcf files at the same time so they can be viewed in separate rows in the vcf panel.
I have supplied artemis a file contiaing the full paths to each vcf file (as per instructions on the artemis website) but only one vcf file is displayed. Has anyone tried to do this?

regards

Brian

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02-08-2011, 07:47 AM	#1
pasta Member Location: Alps Join Date: Jan 2011 Posts: 27	Problem importing BAM files in Artemis Hi there, My first post here and that will be a question. We got data from the Illumina platform and I used BWA to align my reads on the reference genome, which generated BAM files at the end. I would like to visualize my data using Artemis but I cannot load my BAM file. Indeed, I receive this message : "failed to open Organism.pe.bam.SORTED.bam: cannot recognise format of binary file" I dont understand why ... The BAM file seems to be OK since I managed to open it with a bunch of different software. I do have the latest version of Artemis+ACT+ Java, and I did index and sort my BAM file. Any help would be appreciated. Thanks Toni Last edited by pasta; 02-08-2011 at 07:50 AM.

02-08-2011, 08:47 AM	#2
pasta Member Location: Alps Join Date: Jan 2011 Posts: 27	Forget abt my question - I just figured it out myself (whaoo, it took me exactly 1 hour LOL)

02-08-2011, 10:17 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	And what was the solution? Anyone else with the same problem will probably find this thread via Google.

02-09-2011, 12:54 AM	#4
Tani Junior Member Location: singapore Join Date: Dec 2010 Posts: 3	Ensure that the corresponding .bai file in the same directory as of .bam file

02-09-2011, 04:58 AM	#5
pasta Member Location: Alps Join Date: Jan 2011 Posts: 27	I just did something stupid with Artemis... I tried to load the BAM file straight away without any genome loaded first .... I thought it was worth mentioning I was stupid LOL

04-04-2011, 06:32 AM	#6
Trudy Member Location: Italy Join Date: Feb 2011 Posts: 16	How do you solve this problem? I have the same problem..Could you help me? ARTEMIS doesn't load my bam file.. I sorted and indexed the file.bam with samtools.....but the problem persist! help me please....

01-31-2012, 06:26 AM	#8
coldturkey Member Location: Brisbane Join Date: Nov 2008 Posts: 51	I don't have a problem opening bam and vcf files in artemis, however, I would like to open multiple vcf files at the same time so they can be viewed in separate rows in the vcf panel. I have supplied artemis a file contiaing the full paths to each vcf file (as per instructions on the artemis website) but only one vcf file is displayed. Has anyone tried to do this? regards Brian