SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Is it possible to convert a SNP.txt to a bed file or get a SNP.bed from samtools? Ling Bioinformatics 7 04-02-2015 07:17 AM
Updated How to convert .txt file to .bed .GFF or .BAR file format, forevermark4 Bioinformatics 2 06-30-2014 06:02 AM
To convert BAM file to BED file Anjali Bioinformatics 10 04-28-2014 05:43 AM
How to convert BED format to SAM/BAM? seq_newbie Bioinformatics 1 06-23-2011 09:11 AM
How to convert eland file to BED format huo Bioinformatics 1 01-19-2011 11:43 AM

Reply
 
Thread Tools
Old 02-05-2012, 06:12 PM   #1
marufdu07
Junior Member
 
Location: Japan

Join Date: Feb 2012
Posts: 3
Default how to convert SAM file to BED or MUT

Hi all, I am PhD 1st year student, Now working with the high thoughput sequencing data file to search SNPs. I am working with SAM extension file of Chromosome 1 by using IGV 2.0 software. Can anyone give some idea how to convert SAM file to MUT or BED file? I am not sure whether there is any way or not. Regards, Maruf
marufdu07 is offline   Reply With Quote
Old 02-06-2012, 06:36 AM   #2
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default

samtools to go from sam to bam, bedtools bamToBed to go from bam to bed.
mgogol is offline   Reply With Quote
Old 02-07-2012, 03:20 AM   #3
marufdu07
Junior Member
 
Location: Japan

Join Date: Feb 2012
Posts: 3
Default

Hi mgogol,
Thanks for your reply.
where I can get the sam tools or bedtools? How about MUT files?

As mentioned earlier I am IGV 2.0, I tried by using RUN igvtools. I could convert SAM to tdf /idx/sai extension files only.
marufdu07 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 01:04 PM.


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