SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Sam file from alignment of Solid Colorspace reads using Bowtie Alexis1 Bioinformatics 2 02-01-2017 04:51 AM
bowtie priduced SAm file does not have RG tags in alignment neha General 3 03-12-2013 02:47 AM
CIGAR field of SAM file from Bowtie alignment qwsqe Bioinformatics 4 05-08-2012 05:28 AM
wig file generated by MACS doesn`t fit input sam tujchl Bioinformatics 2 06-16-2011 12:23 AM
SAM file from bowtie jay2008 Bioinformatics 0 12-09-2010 05:09 AM

Reply
 
Thread Tools
Old 04-01-2018, 07:27 AM   #1
Pery
Junior Member
 
Location: Israel

Join Date: Apr 2018
Posts: 1
Default Alignment with bowtie doesn't creates .sam file

Hi,

I'm trying to align a fastq.gz file with bowtie.
My script is:
${bowtie_source} --sam --best ${ref_genome} ${fastq_file}

But it doesn't carets a new .sam file.
How to fix the script in order to get a .sam file in a desired directory?
Pery is offline   Reply With Quote
Old 04-02-2018, 07:45 PM   #2
neavemj
Member
 
Location: MA, USA

Join Date: Feb 2014
Posts: 56
Default

I think you need to specify the output file. For example, add "-S new_file.sam" to the script.

Cheers,

Matt.
neavemj is offline   Reply With Quote
Reply

Tags
bowtie, sam

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 07:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO