SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Artemis acceptable input file format problem edge Bioinformatics 13 07-19-2012 04:58 PM
Viewing multiple VCF files in Artemis coldturkey Bioinformatics 0 02-01-2012 02:45 AM
Problem merging BAM files hlwright Bioinformatics 6 10-11-2011 12:36 AM
Failed to View .BAM file in Artemis rururara Bioinformatics 3 04-12-2011 09:38 PM
Size limit for the BAM input of Artemis nivea General 0 04-12-2011 08:38 AM

Reply
 
Thread Tools
Old 02-08-2011, 07:47 AM   #1
pasta
Member
 
Location: Alps

Join Date: Jan 2011
Posts: 27
Question 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.
pasta is offline   Reply With Quote
Old 02-08-2011, 08:47 AM   #2
pasta
Member
 
Location: Alps

Join Date: Jan 2011
Posts: 27
Default

Forget abt my question - I just figured it out myself

(whaoo, it took me exactly 1 hour LOL)
pasta is offline   Reply With Quote
Old 02-08-2011, 10:17 AM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

And what was the solution? Anyone else with the same problem will probably find this thread via Google.
maubp is offline   Reply With Quote
Old 02-09-2011, 12:54 AM   #4
Tani
Junior Member
 
Location: singapore

Join Date: Dec 2010
Posts: 3
Default

Ensure that the corresponding .bai file in the same directory as of .bam file
Tani is offline   Reply With Quote
Old 02-09-2011, 04:58 AM   #5
pasta
Member
 
Location: Alps

Join Date: Jan 2011
Posts: 27
Default

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
pasta is offline   Reply With Quote
Old 04-04-2011, 06:32 AM   #6
Trudy
Member
 
Location: Italy

Join Date: Feb 2011
Posts: 16
Default

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....
Trudy is offline   Reply With Quote
Old 04-04-2011, 08:45 AM   #7
pasta
Member
 
Location: Alps

Join Date: Jan 2011
Posts: 27
Default

Quote:
Originally Posted by Trudy View Post
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
pasta is offline   Reply With Quote
Old 01-31-2012, 06:26 AM   #8
coldturkey
Member
 
Location: Brisbane

Join Date: Nov 2008
Posts: 51
Default

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
coldturkey 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 04:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO