SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
sorting bam files frymor Bioinformatics 23 02-10-2016 06:46 PM
Merging bam files memento Bioinformatics 1 02-17-2012 04:39 PM
Reverse engineering BAM files: BAM -> FASTQ gene coder Bioinformatics 3 01-03-2012 03:42 PM
NEw to Chip-seq and have .bam/.sam/.bam.bai files... then what? NGS newbie Bioinformatics 11 05-25-2011 08:48 AM
Get many Bam Files from 1000genomes dongshong Bioinformatics 0 02-20-2011 08:55 PM

Reply
 
Thread Tools
Old 04-08-2010, 07:58 PM   #1
crisant
Junior Member
 
Location: Rio de Janeiro

Join Date: Mar 2010
Posts: 7
Default help to creat bam files from xls sheets

Hi, people. I would like to know if there is a basic way to convert excel files (few columns, thousands rows) in bam files. One of the column has short reads (~20nt) that I need to see aligned. Is this possible? Thanks for your time.

PD: I dont have deep knowledge in bioinformatics, so if my problem is hard to solve, please indicate me some references to read.
crisant is offline   Reply With Quote
Old 04-09-2010, 07:10 AM   #2
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default

If you need to align the reads, you need to figure out which aligner to use first, like bowtie or bwa or something.

Then you need to figure out what format file those will take, get your reads into that format, run the aligner, and one of the results will be a bam file.
mgogol is offline   Reply With Quote
Old 04-09-2010, 10:37 AM   #3
crisant
Junior Member
 
Location: Rio de Janeiro

Join Date: Mar 2010
Posts: 7
Default

Actually I thought that if I could make a bam file from my xls file, then I could use the Tablet programe. That is the reason why I want to convert to bam. But if I have to use a previous programa (as you said) to the alignement , would I lose the other columns of my xls file? I mean, the ones that have additional information of every read.
crisant is offline   Reply With Quote
Old 04-09-2010, 10:45 AM   #4
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default

On the bedtools mailing list, there was a recent discussion about going from bed (tab-delimited text) to bam. Aaron Quinlan said he might write such software.

I'm not familiar with tablet, but most genome browsers will accept a variety of text based formats, perhaps you could convert your file to one of those other simple formats (bed, gff) or try a different genome browser.
mgogol 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 03:11 AM.


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