SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
SAM/BAM format to wiggle format pinki999 Bioinformatics 19 08-12-2015 01:35 AM
the format of SAM biocc Bioinformatics 6 06-25-2011 10:32 AM
Bowtie/Tophat SAM format detail question traeki Bioinformatics 0 06-12-2011 04:03 PM
Looking process to convert gff3 format into ace format or sam format andylai Bioinformatics 1 05-17-2011 03:09 AM
bowtie - invalid CIGAR string - wrong sam format genome Bioinformatics 2 02-16-2011 02:36 PM

Reply
 
Thread Tools
Old 04-25-2010, 12:27 PM   #1
tninja
Junior Member
 
Location: rockville, MD

Join Date: Apr 2010
Posts: 2
Default anyone help me on bowtie format -> sam format!

Hi all:

I have some bowtie aligned reads with bowtie default .map format and I need to transform them into .sam format. I tried bowtie2sam.pl in samtools/misc directory of samtools package but to my suppriseing the coverted .sam file has no head line and thus cannot be coverted to .bam format and do pileup work further.
Anyone have idea to covert bowtie format to sam format in a right way?

best

Kang Tu
postdoc in NIH
tninja is offline   Reply With Quote
Old 04-25-2010, 01:53 PM   #2
tninja
Junior Member
 
Location: rockville, MD

Join Date: Apr 2010
Posts: 2
Default solved

wrote some script to do that myself...
tninja is offline   Reply With Quote
Old 04-25-2010, 10:33 PM   #3
baby1885
Member
 
Location: china

Join Date: Jan 2010
Posts: 13
Default

You can try 'bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam',the -S option will make output file of sam format.
baby1885 is offline   Reply With Quote
Reply

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 05:25 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO