Question: Help With Sam To Bam
0
gravatar for Zachary A Lewis
6.7 years ago by
Zachary A Lewis10 wrote:
Hi, I was wondering if someone could help me with an error message I'm getting after performing a sam to bam conversion in galaxy. I've used Bowtie to map sequence reads to a custom fasta file corresponding to one chromosome in my organism. The mapping seems to work fine, but when I attempt a sam to bam conversion, I receive the folowing error message: An error occurred running this job: Samtools Version: 0.1.12 (r862) Error creating indexes from reference (/galaxy/main_database/files/002/977/dataset_2977193.dat), [fai_build_core] line length exceeds 65535 in sequence 'LGVII'. Segmentation fault Any help would be appreciated. Thanks, Zack
alignment bowtie samtools bam • 1.3k views
ADD COMMENTlink modified 6.7 years ago by Austin Paul140 • written 6.7 years ago by Zachary A Lewis10
0
gravatar for Austin Paul
6.7 years ago by
Austin Paul140
Austin Paul140 wrote:
You could try "fasta width formatter" on your reference fasta. This has helped me in the past when I received a similar error.
ADD COMMENTlink written 6.7 years ago by Austin Paul140
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 16.09
Traffic: 68 users visited in the last hour