SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Problem with samtools/bcftools alma Bioinformatics 4 01-06-2012 01:40 AM
samtools calmd problem dgtnk Bioinformatics 1 11-29-2011 02:57 AM
SAMTOOLS problem lapti Bioinformatics 1 11-22-2010 08:59 AM
Bowtie + samtools problem scami Bioinformatics 7 09-27-2010 01:03 AM
BWA - Samtools problem joa_ds Bioinformatics 18 11-08-2009 07:55 PM

Reply
 
Thread Tools
Old 06-10-2011, 07:06 AM   #1
Lspoor
Member
 
Location: Fife, Scotland

Join Date: Mar 2010
Posts: 18
Red face samtools.pl pileup2fq problem?

Hi,

I am new to Samtools, and have a problem which I think must be simple to fix!

I am trying to use the following command on my dataset as per the manual:
$ samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq

And get the error:
command not found.

I have tried generating the pileup file separately using Samtools which works fine, so I am assuming I have a problem running the perl script? I have downloaded the latest version of Samtools (v0.1.16), so I guess this means I need to download something else/extra component or a specific perl script in order to get this to work?

Any help appreciated!
Lspoor is offline   Reply With Quote
Old 06-10-2011, 09:27 AM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Do the two parts separately.

You observed that the samtools.pl is by default in the misc folder, not in the same directory as the samtools program itself, right? So probably, the reason it can't find the perl script is because it's not where you told the computer to look.

The samtools.pl script has only one bit that needs to be present to run, Getopt::Std, and I think that's pretty standard. It would tell you that you didn't have it if that were the problem.
swbarnes2 is offline   Reply With Quote
Old 06-10-2011, 09:46 AM   #3
Lspoor
Member
 
Location: Fife, Scotland

Join Date: Mar 2010
Posts: 18
Default Fixed!

And I just realised if I specified the path to samtools.p it worked! PLease delete my thread as it is no longer needed!
Lspoor is offline   Reply With Quote
Reply

Tags
pileup2fq, samtools

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 02:58 AM.


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