Reference file in MapDamge2

SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

For a list of the official rules, visit (https://www.seqanswers.com/forum/sit...wledge-and-win)

See less

Cat_J

Junior Member

Join Date: Oct 2013

Posts: 1
- Share
- Tweet
#1

Reference file in MapDamge2

10-04-2013, 11:14 PM

I am new to bioinformatics, so please forgive me for this simple question!
I am trying to use MapDamage2, and am not sure how to format the reference file. It is currently in .fasta, and was ok the bowtie/samtools pipeline I used, but I don't know how to change it so it works with MapDamage.... any suggestions would be much appreciated.

$ mapDamage -i /Users/name/IonXpress_..._55.sff.raw.bam -r ref.fasta
Error: 'ref.fasta' is not a valid file
Option parsing failed, terminating the program
Tags: adna, mapdamage, ngs
jimmybee

Senior Member

Join Date: Sep 2010

Posts: 119
- Share
- Tweet
#2

10-08-2013, 02:48 AM

Originally posted by Cat_J View Post

I am new to bioinformatics, so please forgive me for this simple question!
I am trying to use MapDamage2, and am not sure how to format the reference file. It is currently in .fasta, and was ok the bowtie/samtools pipeline I used, but I don't know how to change it so it works with MapDamage.... any suggestions would be much appreciated.

$ mapDamage -i /Users/name/IonXpress_..._55.sff.raw.bam -r ref.fasta
Error: 'ref.fasta' is not a valid file
Option parsing failed, terminating the program

Maybe try the full path of the file (like what you did for the input file).
Comment

Previous template Next

A Review of Next-Generation Sequencing Methods for Studying Epigenetics—Part 1

by seqadmin

Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.

Methylation Detect...
- Channel: Articles
05-31-2023, 10:46 AM
Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis

by seqadmin

After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...
- Channel: Articles
05-23-2023, 12:26 PM
Variant Analysis and Genome Assembly: Recommended Tools for Next-Level Sequencing Analysis

by seqadmin

Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.

Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...
- Channel: Articles
05-19-2023, 10:03 AM

Topics	Statistics	Last Post
Genetic Discoveries Transform Our Understanding of Primate Diversity and Behavior by seqadmin Started by seqadmin, Yesterday, 08:56 PM	0 responses 8 views 0 likes	Last Post by seqadmin Yesterday, 08:56 PM
Deep Sequencing Unearths Novel Genetic Variants: Enhancing Precision Medicine for Vascular Anomalies by seqadmin Started by seqadmin, Yesterday, 07:33 AM	0 responses 8 views 0 likes	Last Post by seqadmin Yesterday, 07:33 AM
Unveiling Genetic Associations Through Transcription Factor Binding Quantitative Trait Loci by seqadmin Started by seqadmin, 05-31-2023, 07:50 AM	0 responses 4 views 0 likes	Last Post by seqadmin 05-31-2023, 07:50 AM
Exploring French-Canadian Ancestry: Insights into Migration, Settlement Patterns, and Genetic Structure by seqadmin Started by seqadmin, 05-26-2023, 09:22 AM	0 responses 8 views 0 likes	Last Post by seqadmin 05-26-2023, 09:22 AM

Header Leaderboard Ad

Reference file in MapDamge2

Announcement

SEQanswers June Challenge Has Begun!

Reference file in MapDamge2

Comment

Latest Articles

ad_right_rmr

News