SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK: sorting vcf file given a reference file jorge Bioinformatics 4 01-14-2015 12:16 PM
Reference Gene Sequence file Jluis Bioinformatics 22 12-21-2013 02:21 AM
Bowtie reference genome file alan_sm Illumina/Solexa 0 09-14-2012 02:39 PM
Yeast filter-reference file. fjrossello Bioinformatics 0 01-24-2012 12:22 AM
GS reference Mapper's file nicedad General 3 06-20-2011 07:06 AM

Reply
 
Thread Tools
Old 10-04-2013, 11:14 PM   #1
Cat_J
Junior Member
 
Location: NZ

Join Date: Oct 2013
Posts: 1
Default Reference file in MapDamge2

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
Cat_J is offline   Reply With Quote
Old 10-08-2013, 02:48 AM   #2
jimmybee
Senior Member
 
Location: Adelaide, Australia

Join Date: Sep 2010
Posts: 119
Default

Quote:
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).
jimmybee is offline   Reply With Quote
Reply

Tags
adna, mapdamage, ngs

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 01:12 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO